Microbial community composition and carbon cycling within soil microenvironments of conventional, low-input, and organic cropping systems

Pathways of soil organic carbon accumulation are related to microbial life history strategies in fertilized agroecosystems

Although the formation, turnover, and accumulation of soil organic carbon (SOC) are driven by different fertilizer inputs and their subsequent microbial-mediated transformation, the relationship between changes in plant-derived and microbial-derived components and soil microbial life history strategies under different fertilization regimes has not been well explored. In this study, the changes in microbial necromass carbon (MNC), lignin phenols, and glomalin-related soil protein (GRSP), as well as soil microbial life history strategy were determined in a 16-year field experiment in response to different fertilization regimes, including a no-fertilizer control (C), conventional chemical NPK fertilization (NPK), and partial substitutions of the NPK in chemical fertilizers with a low (30 %) or high (60 %) level of straw (0.3S and 0.6S) or cattle manure (0.3M and 0.6M). The results showed that total lignin phenol content and its contribution to SOC were significantly increased by 88.7 % and 74.2 %, respectively, in high-level straw substitution treatment as compared to chemical fertilization. Both high-level straw and cattle manure substitution increased MNC and total GRSP contents, but did not alter their contributions to SOC compared to chemical fertilization. In fertilized treatments, the high-level cattle manure substitution had the lowest and highest bacterial and fungal K/r ratio, respectively. Bacterial K/r ratio was an important factor in predicting bacterial necromass carbon content and there was a significant negative correlation between them. The ratio of ectomycorrhizal to saprotrophic fungi and fungal diversity were important factors for predicting lignin phenol and GRSP contents, respectively. In addition, the SEMs modeling indicated that straw substitution directly affected lignin phenol and MNC accumulation, whereas cattle manure substitution indirectly affected MNC accumulation by affecting microbial life history strategies. In conclusions, agricultural residues inputs support the formation of a multiple carbon pool of SOC compared to chemical fertilization; and microbial life history strategy is an important driver of SOC formation and affects SOC accumulation and stability in agroecosystems.

Conservation tillage facilitates the accumulation of soil organic carbon fractions by affecting the microbial community in an eolian sandy soil

Conservation tillage (CT) is an important agronomic measure that facilitates soil organic carbon (SOC) accumulation by reducing soil disturbance and plant residue mulching, thus increasing crop yields, improving soil fertility and achieving C neutrality. However, our understanding of the microbial mechanism underlying SOC fraction accumulation under different tillage practices is still lacking. Here, a 6-year in situ field experiment was carried out to explore the effects of CT and traditional tillage (CK) practices on SOC fractions in an eolian sandy soil. Compared with CK, CT increased the particulate OC (POC) content in the 0-30 cm soil layer and the mineral-associated OC (MAOC) content in the 0-20 cm soil layer. Moreover, tillage type and soil depth had significant influences on the bacterial, fungal and protistan community compositions and structures. The co-occurrence network was divided into 4 ecological modules, and module 1 exhibited significant correlations with the POC and MOC contents. After determining their topological roles, we identified the keystone taxa in the network. The results indicated that the most common bacterial taxa may result in SOC loss due to low C use efficiency, while specific fungal (Cephalotrichum) and protistan (Cercozoa) species could facilitate SOC fraction accumulation by promoting macroaggregate formation and predation. Therefore, the increase in keystone fungi and protists, as well as the reduction in bacteria, drove module 1 community function, which in turn promoted SOC sequestration under CT. These results strengthen our understanding of microbial functions in the accrual of SOC fractions, which contributes to the development of conservation agriculture on the Northeast China Plain.

Intercropping on Mars: A promising system to optimise fresh food production in future martian colonies

Future colonists on Mars will need to produce fresh food locally to acquire key nutrients lost in food dehydration, the primary technique for sending food to space. In this study we aimed to test the viability and prospect of applying an intercropping system as a method for soil-based food production in Martian colonies. This novel approach to Martian agriculture adds valuable insight into how we can optimise resource use and enhance colony self-sustainability, since Martian colonies will operate under very limited space, energy, and Earth supplies. A likely early Martian agricultural setting was simulated using small pots, a controlled greenhouse environment, and species compliant with space mission requirements. Pea (Pisum sativum), carrot (Daucus carota) and tomato (Solanum lycopersicum) were grown in three soil types ("MMS-1" Mars regolith simulant, potting soil and sand), planted either mixed (intercropping) or separate (monocropping). Rhizobia bacteria (Rhizobium leguminosarum) were added as the pea symbiont for Nitrogen-fixing. Plant performance was measured as above-ground biomass (g), yield (g), harvest index (%), and Nitrogen/Phosphorus/Potassium content in yield (g/kg). The overall intercropping system performance was calculated as total relative yield (RYT). Intercropping had clear effects on plant performance in Mars regolith, being beneficial for tomato but mostly detrimental for pea and carrot, ultimately giving an overall yield disadvantage compared to monocropping (RYT = 0.93). This effect likely resulted from the observed absence of Rhizobia nodulation in Mars regolith, negating Nitrogen-fixation and preventing intercropped plants from leveraging their complementarity. Adverse regolith conditions-high pH, elevated compactness and nutrient deficiencies-presumably restricted Rhizobia survival/nodulation. In sand, where more favourable soil conditions promoted effective nodulation, intercropping significantly outperformed monocropping (RYT = 1.32). Given this, we suggest that with simple regolith improvements, enhancing conditions for nodulation, intercropping shows promise as a method for optimising food production in Martian colonies. Specific regolith ameliorations are proposed for future research.

Short-term continuous monocropping reduces peanut yield mainly via altering soil enzyme activity and fungal community

Continuous monocropping can lead to soil sickness and increase of soil-borne disease, which finally reduces crop yield. Microorganisms benefit plants by increasing nutrient availability, participating in auxin synthesis, and defending against pathogens. However, little is known about the influence of short-term successive peanuts cropping on soil properties, enzyme activities, its yield, plant-associated microbes, and their potential correlations in peanut production. Here, we examined the community structure, composition, network structure and function of microbes in the rhizosphere and bulk soils under different monocropping years. Moreover, we assessed the impact of changes in the soil micro-environment and associated soil microbes on peanut yield. Our results showed that increase of monocropping year significantly decreased most soil properties, enzyme activities and peanut yield (p < 0.05). Principal co-ordinates analysis (PCoA) and analysis of similarities (ANOSIM) indicated that monocropping year significantly influenced the fungal community structure in the rhizosphere and bulk soils (p < 0.01), while had no effect on the bacterial community. With the increase of continuous monocropping year, peanut selectively decreased (e.g., Candidatus_Entotheonella, Bacillus and Bryobacter) or increased (e.g., Nitrospira, Nocardioides, Ensifer, Gaiella, and Novosphingobium) the abundance of some beneficial bacterial genera in the rhizosphere. Continuous monocropping significantly increased the abundance of plant pathogens (e.g., Plectosphaerella, Colletotrichum, Lectera, Gibberella, Metarhizium, and Microdochium) in the rhizosphere and negatively affected the balance of fungal community. Besides, these species were correlated negatively with L-leucine aminopeptidase (LAP) activity. Network co-occurrence analysis showed that continuous monocropping simplified the interaction network of bacteria and fungi. Random forest and partial least squares path modeling (PLS-PM) analysis further showed that fungal community, pathogen abundance, soil pH, and LAP activity negatively affected peanut yield. In conclusion, short-term continuous monocropping decreased LAP activity and increased potential fungal pathogens abundance, leading to reduction of peanut yield.

Soil microbial diversity and network complexity drive the ecosystem multifunctionality of temperate grasslands under changing precipitation

Soil microbiomes play a critical role in regulating ecosystem multifunctionality. However, whether and how soil protists and microbiome interactions affect ecosystem multifunctionality under climate change is unclear. Here, we transplanted 54 soil monoliths from three typical temperate grasslands (i.e., desert, typical, and meadow steppes) along a precipitation gradient in the Mongolian Plateau and examined their response to nighttime warming, decreased, and increased precipitation. Across the three steppes, nighttime warming only stimulated protistan diversity by 15.61 (absolute change, phylogenetic diversity) but had no effect on ecosystem multifunctionality. Decreased precipitation reduced bacterial (8.78) and fungal (22.28) diversity, but significantly enhanced soil microbiome network complexity by 1.40. Ecosystem multifunctionality was reduced by 0.23 under decreased precipitation, which could be largely attributed to the reduced soil moisture that negatively impacted bacterial and fungal communities. In contrast, increased precipitation had little impact on soil microbial communities. Overall, both bacterial and fungal diversity and network complexity play a fundamental role in maintaining ecosystem multifunctionality in response to drought stress. Protists alter ecosystem multifunctionality by indirectly affecting microbial network complexity. Therefore, not only microbial diversity but also their interactions (regulated by soil protists) should be considered in evaluating the responses of ecosystem multifunctionality, which has important implications for predicting changes in ecosystem functioning under future climate change scenarios.

Rhizosphere soil properties of waxy sorghum under different row ratio configurations in waxy sorghum-soybean intercropping systems

To overcome the continuous planting obstacle and promote the sustainable production of waxy sorghum, a two-years field experiment was performed to determine the responses of waxy sorghum rhizosphere soil properties to different row ratio configurations in waxy sorghum-soybean intercropping systems. The treatments included five row ratio configurations, which were two rows of waxy sorghum intercropped with one row of soybean (2W1S), two rows of waxy sorghum intercropped with two rows of soybean (2W2S), three rows of waxy sorghum intercropped with one row of soybean (3W1S), three rows of waxy sorghum intercropped with two rows of soybean (3W2S), and three rows of waxy sorghum intercropped with three rows of soybean (3W3S), and sole cropping waxy sorghum (SW) was used as control. The nutrients, enzyme activities, and microbes of waxy sorghum rhizosphere soil were investigated at the jointing, anthesis, and maturity stages. Results showed that rhizosphere soil properties of waxy sorghum were significantly affected by row ratio configurations of waxy sorghum intercropped soybean. Among all treatments, the performances of rhizosphere soil nutrients contents, enzymes activities, and microbes contents were 2W1S > 3W1S > 3W2S > 3W3S > 2W2S > SW. Compared to SW treatment, the 2W1S treatment increased the organic matter, total N, total P, total K, gram-negative bacteria phospholipid fatty acids (PLFAs), and gram-positive bacteria PLFAs contents and catalase, polyphenol oxidase, and urease activities by 20.86%-25.67%, 34.33%-70.05%, 23.98%-33.83%, 44.12%-81.86%, 74.87%-194.32%, 81.59-136.59%, 91.44%-114.07%, 85.35%-146.91%, and 36.32%-63.94%, respectively. Likewise, the available N, available P, available K, total PLFAs, fungus PLFAs, actinomycetes PLFAs, and bacteria PLFAs contents under the 2W1S treatment were 1.53-2.41, 1.32-1.89, 1.82-2.05, 1.96-2.91, 3.59-4.44, 9.11-12.56, and 1.81-2.71 times than those of SW treatment, respectively. Further, the determining factors of soil microbes were total K, catalase, and polyphenol oxidase for total microbes, bacteria, and gram-negative bacteria, total P and available K for fungus, available N, available K, and polyphenol oxidase for actinomycetes, and total K and polyphenol oxidase for gram-positive bacteria. In conclusion, the 2W1S treatment was the optimal row ratio configuration of waxy sorghum intercropped with soybean, which can improve the rhizosphere soil quality and promote the sustainable production of waxy sorghum.

Conservation tillage increases surface soil organic carbon stock by altering fungal communities and enzyme activity

Fungal communities play a key role in the decomposition of crop residues and affect soil organic carbon (SOC) dynamics. Conservation tillage enhances SOC sequestration and mitigate global climate change. However, the impact of long-term tillage practices on fungal community diversity and its relation to SOC stock remains unclear. The objectives of this study were to evaluate the relationship between extracellular enzyme activities and fungal community diversity and SOC stock under different tillage practices. A field experiment was conducted with four tillage practices: (i) no-tillage with straw removal (NT0), (ii) no-tillage with straw retention (NTSR, conservation tillage), (iii) plough tillage with straw retention (PTSR), and (iv) rotary tillage with straw retention (RTSR). The results showed that the SOC stock in NTSR was higher than other treatments in the 0-10 cm soil layer. Compared to NT0, NTSR significantly increased soil β-glucosidase, xylosidase, cellobiohydrolase, and chitinase activities at 0-10 cm soil depth (P < 0.05). However, different tillage methods with straw returning had no significant effects on enzyme activity at 0-10 cm soil depth. The observed species and Chao1 index of the fungal communities under NTSR were 22.8% and 32.1% lower than under RTSR in the 0-10 cm soil layer, respectively. The composition, structure, and co-occurrence network of fungal communities differed across tillage practices. A partial least squares path model (PLS-PM) analysis indicated that C-related enzymes were the most influential factors associated with SOC stock. Soil physicochemical properties and fungal communities affected extracellular enzyme activities. Overall, conservation tillage can promote surface SOC stock, which was associated with increased enzyme activity.

Contrasting response of fungal versus bacterial residue accumulation within soil aggregates to long-term fertilization

Soil microorganisms are critical for soil carbon (C) cycling. They primarily regulate the turnover of the soil organic C (SOC) by adjusting their community structure, and contributing residues with a considerable amount to the resistant SOC. Nevertheless, how long-term fertilization (e.g., the combination of manure and chemical fertilizer) affects the spatial distribution of both living microbial communities and dead microbial residue within soil aggregate fractions remains largely unclear. In this study, we analyzed changes in microbial community (lipid biomarkers) and microbial residue retention (amino sugar biomarkers), and also calculated the contribution of microbial residue to organic C in bulk soil and different soil aggregates (> 2 mm, 1-2 mm, 0.25-1 mm, and < 0.25 mm) in Alfisols treated with 29 years fertilization or no fertilization (control). Our results showed that long-term fertilization significantly increased the mean weight diameter (MWD) of aggregates and organic C contents in all aggregate fractions. The fertilization treatment increased the contents of PLFAs and microbial residue C, but the relative contribution of microbial residue to SOC was higher in the control (56.8% vs. 49.0%), due to the low SOC background caused by much lower level of non-microbially derived C input. These results suggested that long-term fertilization could increase SOC by accumulating both plant- and microbial-derived C, while the C deficient soil is more dependent on the accumulation of microbial residues. Long-term fertilization promoted the enrichment of bacterial-derived muramic acid in micro aggregates, but increased the proportion of fungal-derived glucosamine in macro aggregates. Meanwhile, the contribution of bacterial residue to organic C in the fertilization treatment was higher in micro aggregates (7.6% for > 2 mm vs. 9.2% for < 0.25 mm aggregate), while the contribution of fungal residue was higher in macro aggregate fractions (40.9% for > 2 mm vs. 35.7% for < 0.25 mm aggregate). The above results indicated that long-term fertilization could drive the differentiation of heterogeneous microbial residue accumulation patterns that significantly alter the contribution of fungal- versus bacterial-derived C to organic C within soil aggregate fractions.

Soil microbial community assembly and stability are associated with potato (Solanum tuberosum L.) fitness under continuous cropping regime

Continuous cropping obstacles caused by the over-cultivation of a single crop trigger soil degradation, yield reduction and the occurrence of plant disease. However, the relationships among stability, complexity and the assembly process of soil microbial community with continuous cropping obstacles remains unclear. In this study, molecular ecological networks analysis (MENs) and inter-domain ecological networks analysis (IDENs), and a new index named cohesion tools were used to calculate the stability and complexity of soil microbial communities from eight potato cultivars grown under a continuous cropping regime by using the high-throughput sequencing data. The results showed that the stability (i.e., robustness index) of the bacterial and fungal communities for cultivar ZS5 was significantly higher, and that the complexity (i.e., cohesion values) was also significantly higher in the bacterial, fungal and inter-domain communities (i.e., bacterial-fungal community) of cultivar ZS5 than other cultivars. Network analysis also revealed that Actinobacteria and Ascomycota were the dominant phyla within intra-domain networks of continuous cropping potato soil communities, while the phyla Proteobacteria and Ascomycota dominated the correlation of the bacterial-fungal network. Infer community assembly mechanism by phylogenetic-bin-based null model analysis (iCAMP) tools were used to calculate the soil bacterial and fungal communities' assembly processes of the eight potato cultivars under continuous cropping regime, and the results showed that the bacterial community was mainly dominated by deterministic processes (64.19% - 81.31%) while the fungal community was mainly dominated by stochastic processes (78.28% - 98.99%), indicating that the continuous-cropping regime mainly influenced the potato soil bacterial community assembly process. Moreover, cultivar ZS5 possessed a relatively lower homogeneous selection, and a higher TP, TN, AP and yield than other cultivars. Our results indicated that the soil microbial network stability and complexity, and community assemble might be associated with yield and soil properties, which would be helpful in the study for resistance to potato continuous cropping obstacles.

Biochemical composition and function of subalpine shrubland and meadow soil microbiomes in the Qilian Mountains, Qinghai-Tibetan plateau, China

Microorganisms participate in the soil biogeochemical cycle. Therefore, investigating variations in microbial biomass, composition, and functions can provide a reference for improving soil ecological quality due to the sensitivity of microorganisms to vegetation coverage changes. However, the differences in soil microorganisms between shrubland and meadow have not been investigated in ecologically vulnerable subalpine areas. This study aimed to investigate the biochemical composition and functions of the soil microbial community under two shrublands and a meadow at high altitudes (3,400-3,550 m). Three sites under two shrublands, Rhododendron thymifolium (RHO) and Potentilla fruticosa (POT), and one meadow dominated by Kobresia myosuroides (MEA), were selected on the southern slope of the Qilian Mountains on the northeastern edge of the Qinghai-Tibetan Plateau, China. Soil physicochemical properties, the microbial community composition expressed by the phospholipid fatty acid (PLFA) biomarker, and enzyme activities were analyzed as well as their relationships. The results showed that water holding capacity and the soil carbon, nitrogen, and potassium content in RHO and POT were higher than those in the MEA. Moreover, the soil active carbon, dissolved organic carbon, total nitrogen, and dissolved total nitrogen content in RHO were higher than those in POT. The abundance of total PLFAs, bacteria, and fungi beneath the shrublands was considerably higher than that in the MEA. The PLFA abundance in RHO was significantly higher than that in POT. The fungal-to-bacterial ratio of RHO and POT was significantly higher than that in the MEA. The activities of β-glucosidase, cellobiohydrolase, and leucine aminopeptidase were the highest in RHO among the three vegetation types, followed by POT and MEA. The redundancy analysis indicated that the biochemical composition of the soil microorganisms and enzyme activities were driven by total nitrogen, dissolved organic carbon, water holding capacity, and soil organic carbon. Therefore, shrublands, which have higher biomass, can improve soil moisture status, increase soil carbon and nitrogen content (especially active carbon and active nitrogen), and further increase the abundance of total PLFAs, bacteria, and fungi. The increase of microbial biomass indirectly enhances the activity of relevant soil enzymes. The variations in PLFA abundance and enzyme activities can be attributed to shrub species, especially evergreen shrubs, which create more favorable conditions for soil microorganisms. This study provides a theoretical basis for investigating the soil biogeochemical cycle and a scientific basis for soil management and vegetation restoration in the subalpine regions.

High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects

Soil microbial communities play a crucial role in soil fertility, sustainability, and plant health. However, intensive agriculture with increasing chemical inputs and changing environments have influenced native soil microbial communities. Approaches have been developed to study the structure, diversity, and activity of soil microbes to better understand the biology and plant-microbe interactions in soils. Unfortunately, a good understanding of soil microbial community remains a challenge due to the complexity of community composition, interactions of the soil environment, and limitations of technologies, especially related to the functionality of some taxa rarely detected using conventional techniques. Culture-based methods have been shown unable and sometimes are biased for assessing soil microbial communities. To gain further knowledge, culture-independent methods relying on direct analysis of nucleic acids, proteins, and lipids are worth exploring. In recent years, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics have been increasingly used in studying microbial ecology. In this review, we examined the importance of microbial community to soil quality, the mystery of rhizosphere and plant-microbe interactions, and the biodiversity and multi-trophic interactions that influence the soil structure and functionality. The impact of the cropping system and climate change on the soil microbial community was also explored. Importantly, progresses in molecular biology, especially in the development of high-throughput biotechnological tools, were extensively assessed for potential uses to decipher the diversity and dynamics of soil microbial communities, with the highlighted advantages/limitations.

Efficacy of rhizobacterial exopolysaccharides in improving plant growth, physiology, and soil properties

The current study investigated the influence of exopolysaccharides (EPSs) producing plant growth-promoting rhizobacteria (PGPR) on the growth, physiology, and soil properties. The pre-isolated and compatible EPS producing PGPR strains were first screened based on improvement in soil aggregates in an incubation study. The screened strains (Rhizobium phaseoli strain Mn-6, Pseudomonas bathysetes strain LB₅, and unidentified strain R₂) were then employed in pot study for assessing improvements in maize growth, physiology, and soil properties. Eight treatments including T₁ = control, T₂ = Mn-6, T₃ = R₂, T₄ = LB₅, T₅ = Mn-6 + R₂, T₆ = Mn-6 + LB₅, T₇ = R₂ + LB₅, and T₈ = Mn-6 + R₂ + LB₅ were applied in completely randomized design (CRD) hexa replicated (half for root and half for soil, and yield attributes). The results depicted that among various treatments, the application of PGPR strain Mn-6 increased plant height, root length, root fresh and dry weight, root length density, SPAD value, leaf areas index, photosynthesis rate, transpiration, and stomatal conductance by 24, 79, 72, 90, 49, 35, 23, 21, 75, and 77%, respectively, compared with non-inoculated treatment. Similarly, significant improvement in maize yield and soil physical properties was also observed in response to the application of EPS-producing PGPR. Therefore, it is concluded that the application of EPS producing PGPR is an effective strategy to improve plant growth, physiology, yield, and soil physical properties. Moreover, EPS-producing PGPR should be exploited in field studies for their potential in improving plant growth and soil properties.

Soil organic carbon is significantly associated with the pore geometry, microbial diversity and enzyme activity of the macro-aggregates under different land uses

Microbial activity strongly influences the stabilization of soil organic matter (SOM), and is affected by the abiotic properties within soil aggregates, which tend to differ between land uses. Here, we assessed the effects of SOM and pore geometry on the diversity and activity of microbial communities within aggregates formed under different land uses (undisturbed, plantation, pasture, and cropping). X-ray micro-computed tomography (μCT) revealed that macro-aggregates (2-8 mm) of undisturbed soils were porous, highly-connected, and had 200% more macro-pores compared with those from pasture and cropping soils. While the macro-aggregates of undisturbed soils had greater soil organic carbon (SOC) contents and N-acetyl β-glucosaminidase, β-glucosidase, and phosphatase activities, those of cropped soils harboured more diverse bacterial communities. Organic carbon was positively associated with the porosity of the macro-aggregates, which was negatively associated with microbial diversity and positively associated with enzyme activity. Thus, the biophysical processes in macro-aggregates may be important for SOC stabilization within the macro-aggregates.

Diversity and Spatiotemporal Dynamics of Fungal Communities in the Rhizosphere Soil of Cotton in the Arid Region of Northwest China

This study aimed to investigate the fungal diversity and its temporal and spatial dynamics in the rhizosphere soil of healthy cotton by high-throughput sequencing. We studied species richness, composition, and distribution of cotton rhizosphere fungal community with respect to location (Alaer, Kuerle, Tumushuke, Hami, Shihezi, Wusu, and Jinghe) and plant growth period (seedling stage, bud stage, flowering stage, and boll-opening stage) using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. A total of 1,838,454 fungal nuclear ribosomal internal transcribed spacer region sequences (rRNA ITS) were obtained from all cotton plants sampled at different growth stages in the seven locations in Xinjiang. The most abundant fungal group in the cotton rhizosphere was the Ascomycota (78.72%), followed by the Zygomycota (9.56%) and Basidiomycota (2.77%). These sequences revealed an enormous number of operational taxonomic units (OTUs) in cotton (1802 unique OTUs), with 67-464 OTUs in a single cotton sample, at a 3% threshold and a sequencing depth of 30,000 sequences. We identified 33 classes and 389 genera from the resulting 1,800,714 sequences. Sordariomycetes was the most frequent class in all samples, followed by Leotiomycetes and Eurotiomycetes. There were some differences in OTUs among different growth stages, but the differences were not significant, with 382 OTUs (14.66%) being common to each of the stages. A marked difference in the diversity of fungi in the rhizosphere soil of cotton was evident among the different locations, with the highest number of OTUs being detected in Jinghe (1084 OTUs) and clusters of OTUs representative of northern and eastern Xinjiang being detected. There were significantly more tags of Mortierella in Jinghe and Wusu than in the other sampling sites. The dynamics of the rhizosphere fungal communities were influenced by sampling sites. To the best of our knowledge, the current study is the first application of PCR-based Illumina to characterize and compare the fungal biodiversity in multiple rhizosphere soil samples from cotton.

Response of Soil Microbial Communities to Warming and Clipping in Alpine Meadows in Northern Tibet

In order to explore responses of soil microbial communities among different alpine meadows under warming and clipping, soil microorganisms of three alpine meadow sites (low altitude: 4313 m, alpine steppe meadow, 30°30′ N, 91°04′ E; mid-altitude: 4513 m, alpine steppe meadow, 30°31′ N, 91°04′ E; and high altitude: 4693, alpine Kobresia meadow, 30°32′ N, 91°03′ E) were measured using the phospholipid fatty acid (PLFA) method. Both warming and clipping significantly reduced PLFA content and changed the community composition of soil microbial taxa, which belong to bacterial and fungal communities in the alpine Kobresia meadow. Warming significantly reduced the soil total PLFA content by 36.1% and the content of soil fungi by 37.0%; the clipping significantly reduced the soil total PLFA content by 57.4%, the content of soil fungi by 49.9%, and the content of soil bacteria by 60.5% in the alpine Kobresia meadow. Only clipping changed the total fungal community composition at a low altitude. Neither clipping nor warming changed the microbial community composition at a moderate altitude. Soil temperature, soil moisture, and pH were the main factors affecting soil microbial communities. Therefore, the effects of warming and clipping on soil microbial communities in alpine meadows were related to grassland types and soil environmental conditions.

Cow manure application effectively regulates the soil bacterial community in tea plantation

Background

Cow manure is not only an agricultural waste, but also an organic fertilizer resource. The application of organic fertilizer is a feasible practice to mitigate the soil degradation caused by overuse of chemical fertilizers, which can affect the bacterial diversity and community composition in soils. However, to our knowledge, the information about the soil bacterial diversity and composition in tea plantation applied with cow manure fertilization was limited. In this study, we performed one field trial to research the response of the soil bacterial community to cow manure fertilization compared with urea fertilization using the high-throughput sequencing technique of 16S rRNA genes, and analyzed the relationship between the soil bacterial community and soil characteristics during different tea-picking seasons using the Spearman’s rank correlation analysis.

Results

The results showed that the soil bacterial communities were dominated by Proteobacteria, Bacteroidetes, Acidobacteria and Actinobacteria across all tea-picking seasons. Therein, there were significant differences of bacterial communities in soils with cow manure fertilization (CMF) and urea fertilization (UF) in three seasons: the relative abundance of Bacteroidetes in CMF was significantly higher than that in UF and CK in spring, and the relative abundance of Proteobacteria and Bacteroidetes in CMF was significantly higher than that in UF and CK in autumn. So, the distribution of the dominant phyla was mainly affected by cow manure fertilization. The diversity of bacterial communities in soils with cow manure fertilization was higher than that in soils with urea fertilization, and was the highest in summer. Moreover, soil pH, OM and AK were important environmental properties affecting the soil bacterial community structure in tea plantation.

Conclusions

Although different fertilizers and seasons affect the diversity and structure of soil microorganisms, the application of cow manure can not only improve the diversity of soil bacteria, but also effectively regulate the structure of soil bacterial community in tea plantation. So, cow manure fertilization is more suitable for tea plantation.

Mixing effect of polylactic acid microplastic and straw residue on soil property and ecological function

Microplastics have become a contaminant of increasing concern in soils. Although biodegradable plastics were considered as alternatives of traditional plastics, some evidence showed that biodegradable plastics might produce more microplastics. Until now, the effect of biodegradable microplastics on soil functions and processes, as well as microbial communities is uncertain. Based on high throughput sequencing, enzymatic activity assay and dynamic analysis of soil carbon and nitrogen, we investigated the effects of biodegradable polylactic acid microplastics (PLA MPs) on soil microbiota and related ecological processes under conditions of high or low carbon content. The results showed that PLA MPs had no significant effect on the overall diversity and composition of bacterial communities or related ecosystem functions and processes. However, co-occurrence network analysis revealed that PLA MPs impacted the interactions between constituent species, which might have legacy effect on soil bacterial communities and functions. Our data also revealed that PLA MPs could trade off the priming effect of carbon source. Our results provided an integrated picture in understanding the effects of PLA MPs on soil microbes, properties and ecological functions, which will help to further understand the effects of MPs on terrestrial ecosystems.

The potential of corn-soybean intercropping to improve the soil health status and biomass production in cool climate boreal ecosystems

Intercropping (IC) is a promising approach used to improve soil health and sustainable crop production. However, it is unknown whether IC improve the soil health status and biomass productivity of crops cultivated in podzols under cool climate in boreal ecosystems. Two silage corn and three forage soybean genotypes were cultivated either as inter or monocrop (MC) treatments in a randomized complete block design. IC resulted in 28% increase in total forage production (FP). A reduction in rhizosphere soil pH (RS-pH) was observed in the IC treatments. Conversely, the rhizosphere soil acid phosphatase (RS-APase) activity was significantly higher (26-46%) in the IC treatments and occurred concomitant with a significant increase in available phosphorus (RS-Pavailable) (26-74%) in the rhizosphere. Furthermore, IC enhanced the active microbial composition and strong positive correlations were observed between RS-Pavailable, RS-APase, microbial biomass and FP; while RS-pH was negatively correlated with FP, RS-APase and RS-Pavailable. These findings suggested silage corn intercropped with forage soybean could be a viable approach to enhance FP through improved active microbial community structure, RS-APase activity and RS-Pavailable when cultivated on podzols in cool climate boreal ecosystem.

Interaction Between Conservation Tillage and Nitrogen Fertilization Shapes Prokaryotic and Fungal Diversity at Different Soil Depths: Evidence From a 23-Year Field Experiment in the Mediterranean Area

Soil biodiversity accomplishes key roles in agro-ecosystem services consisting in preserving and enhancing soil fertility and nutrient cycling, crop productivity and environmental protection. Thus, the improvement of knowledge on the effect of conservation practices, related to tillage and N fertilization, on soil microbial communities is critical to better understand the role and function of microorganisms in regulating agro-ecosystems. In the Mediterranean area, vulnerable to climate change and suffering for management-induced losses of soil fertility, the impact of conservation practices on soil microbial communities is of special interest for building mitigation and adaptation strategies to climate change. A long-term experiment, originally designed to investigate the effect of tillage and N fertilization on crop yield and soil organic carbon, was utilized to understand the effect of these management practices on soil prokaryotic and fungal community diversity. The majority of prokaryotic and fungal taxa were common to all treatments at both soil depths, whereas few bacterial taxa (Cloacimonates, Spirochaetia and Berkelbacteria) and a larger number of fungal taxa (i.e., Coniphoraceae, Debaryomycetaceae, Geastraceae, Cordicypitaceae and Steccherinaceae) were unique to specific management practices. Soil prokaryotic and fungal structure was heavily influenced by the interaction of tillage and N fertilization: the prokaryotic community structure of the fertilized conventional tillage system was remarkably different respect to the unfertilized conservation and conventional systems in the surface layer. In addition, the effect of N fertilization in shaping the fungal community structure of the surface layer was higher under conservation tillage systems than under conventional tillage systems. Soil microbial community was shaped by soil depth irrespective of the effect of plowing and N addition. Finally, chemical and enzymatic parameters of soil and crop yields were significantly related to fungal community structure along the soil profile. The findings of this study gave new insights on the identification of management practices supporting and suppressing beneficial and detrimental taxa, respectively. This highlights the importance of managing soil microbial diversity through agro-ecological intensified systems in the Mediterranean area.

Yields and resilience outcomes of organic, cover crop, and conventional practices in a Mediterranean climate

Adaptive management practices that maximize yields while improving yield resilience are required in the face of resource variability and climate change. Ecological intensification such as organic farming and cover cropping are lauded in some studies for fostering yield resilience, but subject to criticism in others for their low productivity. We implemented a quantitative framework to assess yield resilience, emphasizing four aspects of yield dynamics: yield, yield stability, yield resistance (i.e., the ability of systems to avoid crop failure under stressful growing conditions), and maximum yield potential. We compared the resilience of maize-tomato rotation systems after 24 years of irrigated organic, cover cropped, and conventional management in a Mediterranean climate, and identified crop-specific resilience responses of tomato and maize to three management systems. Organic management maintained tomato yields comparable to those under conventional management, while increasing yield stability and resistance. However, organic and cover cropped system resulted in 36.1% and 35.8% lower maize yields and reduced yield stability and resistance than the conventional system. Our analyses suggest that investments in ecological intensification approaches could potentially contribute to long-term yield resilience, however, these approaches need to be tailored for individual crops and systems to maximize their benefits, rather than employing one-size-fits-all approaches.

Effects of fumigation with 1,3-dichloropropene on soil enzyme activities and microbial communities in continuous-cropping soil

The compound 1,3-D (1,3-dichloropropene) is a potential candidate soil fumigant due to the restrictions on methyl bromide (MB). To date, little is known about the soil microbial community changes induced by 1,3-D fumigation. Therefore, soil properties, related soil enzymes, genes encoding the key enzymes of ammonia oxidation in both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) and bacterial diversity were investigated to assess the effects of 1,3-D fumigation on the soil microbial community. The results exhibited that fumigation with 1,3-D caused accumulation of NH₄⁺-N, but it led to decrease in the rate of NO₃^--N, and the concentration of NO₃^--N gradually recovered. At 12 weeks after transplant (WAT) of tomato seedlings, the concentration of NH₄⁺-N and NO₃^--N were not statistically significant between the 1,3-D treatment groups and the untreated control group. A similar tendency was found for organic matter, soil pH, urease and protease activities. Moreover, quantitative real-time PCR (qPCR) showed that 1,3-D decreased total bacterial abundance, AOA-amoA and AOB-amoA genes. In addition, Illumina MiSeq sequencing analysis revealed that soil bacterial community diversities were significantly reduced at earlier sampling time points, and at later sampling time points, soil bacterial diversity gradually recovered, there was no significant difference compared to the control group. The present study provides useful information to evaluate the environmental safety of 1,3-D.

Toxicity responses of bacterial community as a biological indicator after repeated exposure to lead (Pb) in the presence of decabromodiphenyl ether (BDE209)

Continuous exposure of chemicals could cause various environmental impacts. Decabromodiphenyl ether (BDE209) and lead (Pb) can co-exist and are discharged simultaneously at e-waste recycling sites (EWRSs). Extensive concerns have been attracted by their toxic effects on soil microorganisms. Thus, by using high-throughput sequencing, this study explored bacterial community responses in a soil system after repeated Pb exposure in the presence of BDE209 in the laboratory during 90-day indoor incubation period. Gene sequencing of 16S rDNA performed on an Illumina MiSeq platform proved that one-off Pb exposure caused higher microbial abundance and community diversity. Additionally, both repetitive Pb treatment and exogenous BDE209 input could change bacterial community composition. Twenty-three different bacterial phyla were detected in the soil samples, while more than 90% of the sequences in each treatment belonged to a narrow variety. The sequence analyses elucidated that Proteobacteria, Acidobacteria, and Bacteroidetes were the top three dominant phyla. Our observations could provide a few insights into the ecological risks of Pb and BDE209 co-existed contamination in soils at EWRSs.

Responses of soil microbial community structure changes and activities to biochar addition: A meta-analysis

The objective of this study was to investigate responses of soil microbial community structure changes and activities to biochar addition under different biochar characteristics, soil properties, and experiment conditions. A meta-analysis was conducted based on 265 datasets from 49 published studies. Results showed that biochar addition significantly increased the ratios of soil fungi to bacteria (F/B) and the ratios of Gram-positive bacteria to Gram-negative bacteria (G+/G-), and microbial biomass and activities. The enhancement of F/B ratios was most significant with addition of biochars produced at low temperatures to soils with lower pH and nutrients in a long-term condition, which improved ecosystem stability of agricultural soils. The F/B ratios were mainly affected by biochar nutrients, soil nutrients, and soil pH values. Biochar nutrients and structural properties (i.e., surface area and porosity) also played the important role in enhancing G+/G-, total microbial biomass, and activities of bacteria, fungi, and actinomycetes. The G+/G- ratios increased the most with addition of biochars produced with medium temperatures and residue accompanied with fertilizers in dry land (dried farmland) soils. High biochar load greatly improved the total phospholipid fatty acids, and activities of bacteria, fungi, and actinomycetes in fine/coarse, paddy soils, and soils with low nutrients, in turn increased the soil nutrient cycling. In addition, the structural properties of biochars were the most influencing factor to increase total microbial biomass and actinomycete activity. Overall, the enhancement of microbial activities and community structure shifts under biochar addition should promote soil nutrients cycling and carbon sequestration, and improve crop yields.

Response of Organic Matter Decomposition to No-Tillage Adoption Evaluated by the Tea Bag Technique

Organic matter (OM) decomposition is a fundamental ecosystem service in conservation agriculture, but the response of this process to the conversion from conventional tillage (CT) to no-tillage (NT) systems is not fully understood, especially during the transition period. Here, using a litterbag experiment (tea bag technique), we studied OM decomposition in a chronosequence of NT fields of different ages since conversion from CT (1 to 7 years) around Beauvais (northern France). We found that, in contrast with physico-chemical soil properties, the decomposition of both high quality (green tea) and low quality (rooibos tea) organic matter was significantly correlated with the NT age. Irrespective of the OM quality, the OM mass losses linearly increased with the time span since conversion from CT to NT. Taken together, our results suggest that adopting NT practices provides more favorable habitats for microorganisms involved in OM decomposition.

Contrasting beneficial and pathogenic microbial communities across consecutive cropping fields of greenhouse strawberry

Soil weakness across consecutive cropping fields can be partially explained by the changes in microbial community diversity and structure. Succession patterns and co-occurrence mechanisms of bacteria and fungi, especially beneficial or pathogenic memberships in continuous cropping strawberry fields and their response to edaphic factors remained unclear. In this study, Illumina sequencing of bacterial 16S ribosomal RNA and fungal internal transcribed spacer genes was applied in three time-course (1, 5, and 10 years) fields across spring and winter. Results showed that the richness and diversity of bacterial and fungal communities increased significantly (p < 0.05) in 1-year field and decreased afterwards across two seasons. Network analysis revealed beneficial bacterial and fungal genus (Bacillus and Trichoderma) dominated under 1-year field whereas Fusarium accumulated under 10-year field at either season. Moreover, Trichoderma harzianum and Bacillus subtilis that have been reported to effectively control Fusarium wilt in strawberries accumulated significantly under 1-year field. Canonical correspondence analysis showed that beneficial bacterial Rhodospirillales and Rhizobiales and fungal Glomerales accumulated in 1-year field and their distributions were significantly affected by soil pH, microbial biomass C (MBC), and moisture. On the contrary, fungal pathogenic species Fusarium oxysporum strongly increased under 10-year field at the winter sample and the abundance was positively (p < 0.01) correlated with soil moisture. Our study suggested that the potential of microcosm under 1-year field stimulates the whole microbial diversity and favors different beneficial taxa across two seasons. Soil pH, moisture, and MBC were the most important edaphic factors leading to contrasting beneficial and pathogenic memberships across consecutive strawberry cropping fields.

Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil

Reducing tillage and growing cover crops, widely recommended practices for boosting soil health, have major impacts on soil communities. Surprisingly little is known about their impacts on soil microbial functional diversity, and especially so in irrigated Mediterranean ecosystems. In long-term experimental plots at the West Side Research and Extension Center in California's Central Valley, we characterized soil microbial communities in the presence or absence of physical disturbance due to tillage, in the presence or absence of cover crops, and at three depths: 0-5, 5-15 and 15-30 cm. This characterization included qPCR for bacterial and archaeal abundances, DNA sequencing of the 16S rRNA gene, and phylogenetic estimation of two ecologically important microbial traits (rRNA gene copy number and genome size). Total (bacterial + archaeal) diversity was higher in no-till than standard till; diversity increased with depth in no-till but decreased with depth in standard till. Total bacterial numbers were higher in cover cropped plots at all depths, while no-till treatments showed higher numbers in 0-5 cm but lower numbers at lower depths compared to standard tillage. Trait estimates suggested that different farming practices and depths favored distinctly different microbial life strategies. Tillage in the absence of cover crops shifted microbial communities towards fast growing competitors, while no-till shifted them toward slow growing stress tolerators. Across all treatment combinations, increasing depth resulted in a shift towards stress tolerators. Cover crops shifted the communities towards ruderals-organisms with wider metabolic capacities and moderate rates of growth. Overall, our results are consistent with decreasing nutrient availability with soil depth and under no-till treatments, bursts of nutrient availability and niche homogenization under standard tillage, and increases in C supply and variety provided by cover crops. Understanding how agricultural practices shift microbial abundance, diversity and life strategies, such as presented here, can assist with designing farming systems that can support high yields, while enhancing C sequestration and increasing resilience to climate change.

Resource Legacies of Organic and Conventional Management Differentiate Soil Microbial Carbon Use

Long-term contrasts in agricultural management can shift soil resource availability with potential consequences to microbial carbon (C) use efficiency (CUE) and the fate of C in soils. Isothermal calorimetry was combined with ¹³C-labeled glucose stable isotope probing (SIP) of 16S rRNA genes to test the hypothesis that organically managed soils would support microbial communities with greater thermodynamic efficiency compared to conventional soils due to a legacy of lower resource availability and a resultant shift toward communities supportive of more oligotrophic taxa. Resource availability was greater in conventionally managed soils, with 3.5 times higher available phosphorus, 5% more nitrate, and 36% more dissolved organic C. The two management systems harbored distinct glucose-utilizing populations of Proteobacteria and Actinobacteria, with a higher Proteobacteria:Actinobacteria ratio (2.4 vs. 0.7) in conventional soils. Organically managed soils also harbored notable activity of Firmicutes. Thermodynamic efficiency indices were similar between soils, indicating that glucose was metabolized at similar energetic cost. However, differentially abundant glucose utilizers in organically managed soils were positively correlated with soil organic matter (SOM) priming and negatively correlated to soil nutrient and carbon availability, respiration, and heat production. These correlation patterns were strongly reversed in the conventionally managed soils indicating clear differentiation of microbial functioning related to soil resource availability. Fresh C addition caused proportionally more priming of SOM decomposition (57 vs. 51%) in organically managed soils likely due to mineralization of organic nutrients to satisfy microbial demands during glucose utilization in these more resource deprived soils. The additional heat released from SOM oxidation may explain the similar community level thermodynamic efficiencies between management systems. Restoring fertility to soils with a legacy of nutrient limitation requires a balanced supply of both nutrients and energy to protect stable SOM from microbial degradation. These results highlight the need to consider managing C for the energy it provides to ıcritical biological processes that underpin soil health.

Microbial Functional Diversity, Biomass and Activity as Affected by Soil Surface Mulching in a Semiarid Farmland

Mulching is widely used to increase crop yield in semiarid regions in northwestern China, but little is known about the effect of different mulching systems on the microbial properties of the soil, which play an important role in agroecosystemic functioning and nutrient cycling. Based on a 4-year spring maize (Zea mays L.) field experiment at Changwu Agricultural and Ecological Experimental Station, Shaanxi, we evaluated the responses of soil microbial activity and crop to various management systems. The treatments were NMC (no mulching with inorganic N fertilizer), GMC (gravel mulching with inorganic N fertilizer), FMC (plastic-film mulching with inorganic N fertilizer) and FMO (plastic-film mulching with inorganic N fertilizer and organic manure addition). The results showed that the FMO soil had the highest contents of microbial biomass carbon and nitrogen, dehydrogenase activity, microbial activity and Shannon diversity index. The relative use of carbohydrates and amino acids by microbes was highest in the FMO soil, whereas the relative use of polymers, phenolic compounds and amines was highest in the soil in the NMC soil. Compared with the NMC, an increased but no significant trend of biomass production and nitrogen accumulation was observed under the GMC treatment. The FMC and FMO led a greater increase in biomass production than GMC and NMC. Compare with the NMC treatment, FMC increased grain yield, maize biomass and nitrogen accumulation by 62.2, 62.9 and 86.2%, but no significant difference was found between the FMO and FMC treatments. Some soil biological properties, i.e. microbial biomass carbon, microbial biomass nitrogen, being sensitive to the mulching and organic fertilizer, were significant correlated with yield and nitrogen availability. Film mulching over gravel mulching can serve as an effective measure for crop production and nutrient cycling, and plus organic fertilization additions may thus have improvements in the biological quality of the soil and its sustainability in the rainfall-limited semiarid region.

Soil Functional Zone Management: A Vehicle for Enhancing Production and Soil Ecosystem Services in Row-Crop Agroecosystems

There is increasing global demand for food, bioenergy feedstocks and a wide variety of bio-based products. In response, agriculture has advanced production, but is increasingly depleting soil regulating and supporting ecosystem services. New production systems have emerged, such as no-tillage, that can enhance soil services but may limit yields. Moving forward, agricultural systems must reduce trade-offs between production and soil services. Soil functional zone management (SFZM) is a novel strategy for developing sustainable production systems that attempts to integrate the benefits of conventional, intensive agriculture, and no-tillage. SFZM creates distinct functional zones within crop row and inter-row spaces. By incorporating decimeter-scale spatial and temporal heterogeneity, SFZM attempts to foster greater soil biodiversity and integrate complementary soil processes at the sub-field level. Such integration maximizes soil services by creating zones of 'active turnover', optimized for crop growth and yield (provisioning services); and adjacent zones of 'soil building', that promote soil structure development, carbon storage, and moisture regulation (regulating and supporting services). These zones allow SFZM to secure existing agricultural productivity while avoiding or minimizing trade-offs with soil ecosystem services. Moreover, the specific properties of SFZM may enable sustainable increases in provisioning services via temporal intensification (expanding the portion of the year during which harvestable crops are grown). We present a conceptual model of 'virtuous cycles', illustrating how increases in crop yields within SFZM systems could create self-reinforcing feedback processes with desirable effects, including mitigation of trade-offs between yield maximization and soil ecosystem services. Through the creation of functionally distinct but interacting zones, SFZM may provide a vehicle for optimizing the delivery of multiple goods and services in agricultural systems, allowing sustainable temporal intensification while protecting and enhancing soil functioning.

Effects of Intercropping with Potato Onion on the Growth of Tomato and Rhizosphere Alkaline Phosphatase Genes Diversity

BACKGROUND AND AIMS

In China, excessive fertilization has resulted in phosphorus (P) accumulation in most greenhouse soils. Intercropping can improve the efficiency of nutrient utilization in crop production. In this study, pot experiments were performed to investigate the effects of intercropping with potato onion (Allium cepa L. var. aggregatum G. Don) on tomato (Solanum lycopersicum L.) seedlings growth and P uptake, the diversity of rhizosphere phosphobacteria and alkaline phosphatase (ALP) genes in phosphorus-rich soil.

METHODS

The experiment included three treatments, namely tomato monoculture (TM), potato onion monoculture (OM), and tomato/potato onion intercropping (TI-tomato intercropping and OI-potato onion intercropping). The growth and P uptake of tomato and potato onion seedlings were evaluated. The dilution plating method was used to determine the population of phosphate-solubilizing bacteria (PSB) and phosphate-mineralizing bacteria (PMB). The genomic DNAs of PSB and PMB in the rhizosphere of tomato and potato onions were extracted and purified, and then, with the primer set of 338f /518r, the PCR amplification of partial bacterial 16S rDNA sequence was performed and sequenced to determine the diversities of PSB and PMB. After extracting the total genomic DNAs from the rhizosphere, the copy numbers and diversities of ALP genes were investigated using real-time PCR and PCR-DGGE, respectively.

RESULTS

Intercropping with potato onion promoted the growth and P uptake of tomato seedlings, but inhibited those of potato onion. After 37 days of transplanting, compared to the rhizosphere of TM, the soil pH increased, while the electrolytic conductivity and Olsen P content decreased (p < 0.05) in the rhizosphere of TI. The populations and diversities of PSB, PMB, and ALP genes increased significantly in the rhizosphere of TI, compared to the rhizosphere of TM.

CONCLUSION

The results indicated that intercropping with potato onion promoted the growth and P uptake of tomato in phosphorus-rich soil and affected the community structure and function of phosphobacteria in tomato rhizosphere. Intercropping with potato onion also improved soil quality by lowering levels of soil acidification and salinization.

Long-term impact of farm management and crops on soil microorganisms assessed by combined DGGE and PLFA analyses

In the present study, long-term organic and conventional managements were compared at the experimental field of Monsampolo del Tronto (Marche region, Italy) with the aim of investigating soil chemical fertility and microbial community structure. A polyphasic approach, combining soil fertility indicators with microbiological analyses (plate counts, PCR-denaturing gradient gel electrophoresis [DGGE] and phospholipid fatty acid analysis [PLFA]) was applied. Organic matter, N as well as some important macro and micronutrients (K, P, Mg, Mn, Cu, and Zn) for crop growth, were more available under organic management. Bacterial counts were higher in organic management. A significant influence of management system and management x crop interaction was observed for total mesophilic bacteria, nitrogen fixing bacteria and actinobacteria. Interestingly, cultivable fungi were not detected in all analyzed samples. PLFA biomass was higher in the organic and Gram positive bacteria dominated the microbial community in both systems. Even if fungal biomass was higher in organic management, fungal PCR-DGGE fingerprinting revealed that the two systems were very similar in terms of fungal species suggesting that 10 years were not enough to establish a new dynamic equilibrium among ecosystem components. A better knowledge of soil biota and in particular of fungal community structure will be useful for the development of sustainable management strategies.

Similar processes but different environmental filters for soil bacterial and fungal community composition turnover on a broad spatial scale

Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km²): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landes<Burgundy≤Brittany<<South-East) using the systematic grid of French Soil Quality Monitoring Network to evaluate the communities’ composition turnovers. The relative importance of processes and filters was assessed by distance-based redundancy analysis. This study demonstrates significant community composition turnover rates for soil bacteria and fungi, which were dependent on the region. Bacterial and fungal community composition turnovers were mainly driven by environmental selection explaining from 10% to 20% of community composition variations, but spatial variables also explained 3% to 9% of total variance. These variables highlighted significant spatial autocorrelation of both communities unexplained by the environmental variables measured and could partly be explained by dispersal limitations. Although the identified filters and their hierarchy were dependent on the region and organism, selection was systematically based on a common group of environmental variables: pH, trophic resources, texture and land use. Spatial autocorrelation was also important at coarse (80 to 120 km radius) and/or medium (40 to 65 km radius) spatial scales, suggesting dispersal limitations at these scales.

Does agricultural crop diversity enhance soil microbial biomass and organic matter dynamics? A meta-analysis

Our increasing dependence on a small number of agricultural crops, such as corn, is leading to reductions in agricultural biodiversity. Reductions in the number of crops in rotation or the replacement of rotations by monocultures are responsible for this loss of biodiversity. The belowground implications of simplifying agricultural plant communities remain unresolved; however, agroecosystem sustainability will be severely compromised if reductions in biodiversity reduce soil C and N concentrations, alter microbial communities, and degrade soil ecosystem functions as reported in natural communities. We conducted a meta-analysis of 122 studies to examine crop rotation effects on total soil C and N concentrations, and the faster cycling microbial biomass C and N pools that play key roles in soil nutrient cycling and physical processes such as aggregate formation. We specifically examined how rotation crop type and management practices influence C and N dynamics in different climates and soil types. We found that adding one or more crops in rotation to a monoculture increased total soil C by 3.6% and total N by 5.3%, but when rotations included a cover crop (i.e., crops that are not harvested but produced to enrich the soil and capture inorganic N), total C increased by 8.5% and total N 12.8%. Rotations substantially increased the soil microbial biomass C (20.7%) and N (26.1%) pools, and these overwhelming effects on microbial biomass were not moderated by crop type or management practices. Crop rotations, especially those that include cover crops, sustain soil quality and productivity by enhancing soil C, N, and microbial biomass, making them a cornerstone for sustainable agroecosystems.

The effects of fencing on carbon stocks in the degraded alpine grasslands of the Qinghai-Tibetan Plateau

Quantifying the carbon storage of grasslands under different management strategies can help us understand how this ecosystem responds to different land management practices. To assess the C cycle and the importance of soil microbial biomass carbon, we measured the levels of soil organic carbon, biomass carbon (above- and underground) and soil microbial biomass carbon in areas with different grazing intensities and different management strategy (fenced and unfenced) in the Qinghai-Tibetan Plateau. We also calculated the ratio of soil microbial biomass carbon to soil organic carbon as an indicator of the soil organic matter availability and quality. Results showed that degradation had significant effects on the soil organic carbon, biomass carbon and microbial biomass carbon (P < 0.05). However, fencing only had a significant effect on the non-degraded and moderately degraded grasslands (P < 0.05). We also found that the level of soil microbial biomass carbon was positively correlated with the biomass carbon and soil organic carbon. From our research, we concluded that the level of soil microbial biomass carbon was crucial to the C cycle in the alpine grasslands and that fencing may be an important management strategy for restoring lightly or moderately degraded grassland in the Qinghai-Tibetan Plateau.

Functional gene differences in soil microbial communities from conventional, low-input, and organic farmlands

Various agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO(3)(-), NH(4)(+), available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO(3)(-) concentration and denitrification genes, NH(4)(+) concentration and ammonification genes, and N(2)O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes.

Experimental litterfall manipulation drives large and rapid changes in soil carbon cycling in a wet tropical forest

Global changes such as variations in plant net primary production are likely to drive shifts in leaf litterfall inputs to forest soils, but the effects of such changes on soil carbon (C) cycling and storage remain largely unknown, especially in C-rich tropical forest ecosystems. We initiated a leaf litterfall manipulation experiment in a tropical rain forest in Costa Rica to test the sensitivity of surface soil C pools and fluxes to different litter inputs. After only 2 years of treatment, doubling litterfall inputs increased surface soil C concentrations by 31%, removing litter from the forest floor drove a 26% reduction over the same time period, and these changes in soil C concentrations were associated with variations in dissolved organic matter fluxes, fine root biomass, microbial biomass, soil moisture, and nutrient fluxes. However, the litter manipulations had only small effects on soil organic C (SOC) chemistry, suggesting that changes in C cycling, nutrient cycling, and microbial processes in response to litter manipulation reflect shifts in the quantity rather than quality of SOC. The manipulation also affected soil CO 2 fluxes; the relative decline in CO 2 production was greater in the litter removal plots (-22%) than the increase in the litter addition plots (+15%). Our analysis showed that variations in CO 2 fluxes were strongly correlated with microbial biomass pools, soil C and nitrogen (N) pools, soil inorganic P fluxes, dissolved organic C fluxes, and fine root biomass. Together, our data suggest that shifts in leaf litter inputs in response to localized human disturbances and global environmental change could have rapid and important consequences for belowground C storage and fluxes in tropical rain forests, and highlight differences between tropical and temperate ecosystems, where belowground C cycling responses to changes in litterfall are generally slower and more subtle.