Response of soil microbial biomass and community structures to conventional and organic farming systems under identical crop rotations

In this study the influence of different farming systems on microbial community structure was analyzed using soil samples from the DOK long-term field experiment in Switzerland, which comprises organic (BIODYN and BIOORG) and conventional (CONFYM and CONMIN) farming systems as well as an unfertilized control (NOFERT). We examined microbial communities in winter wheat plots at two different points in the crop rotation (after potatoes and after maize). Employing extended polar lipid analysis up to 244 different phospholipid fatty acids (PLFA) and phospholipid ether lipids (PLEL) were detected. Higher concentrations of PLFA and PLEL in BIODYN and BIOORG indicated a significant influence of organic agriculture on microbial biomass. Farmyard manure (FYM) application consistently revealed the strongest, and the preceding crop the weakest, influence on domain-specific biomass, diversity indices and microbial community structures. Esterlinked PLFA from slowly growing bacteria (k-strategists) showed the strongest responses to long-term organic fertilization. Although the highest fungal biomass was found in the two organic systems of the DOK field trial, their contribution to the differentiation of community structures according to the management regime was relatively low. Prokaryotic communities responded most strongly to either conventional or organic farming management.     

Soil Microbial Substrate Properties and Microbial Community Responses under Irrigated Organic and Reduced-Tillage Crop and Forage Production Systems

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

Diversity and activity of free-living nitrogen-fixing bacteria and total bacteria in organic and conventionally managed soils

Agricultural soils are heterogeneous environments in which conditions affecting microbial growth and diversity fluctuate widely in space and time. In this study, the molecular ecology of the total bacterial and free-living nitrogen-fixing communities in soils from the Nafferton Factorial Systems Comparison (NFSC) study in northeast England were examined. The field experiment was factorial in design, with organic versus conventional crop rotation, crop protection, and fertility management factors. Soils were sampled on three dates (March, June, and September) in 2007. Total RNA was extracted from all soil samples and reverse transcribed. Denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) were used to analyze nifH and 16S rRNA genes in order to study free-living diazotrophs and the total bacterial community, respectively. Crop rotation was shown to have a significant effect on total bacterial diversity (and that of free-living N fixers) (P ≤ 0.001). On all three dates, nifH activity was higher in the conventional crop rotation. In contrast, qPCR analysis of free-living N fixers indicated significantly higher levels of activity in conventionally fertilized plots in June (P = 0.0324) and in plots with organic crop protection in September (P = 0.0143). To our knowledge, the effects of organic and conventional farming systems on free-living diazotrophs have never been studied. An increased understanding of the impacts of management practices on free-living N fixers could allow modifications in soil management practices to optimize the activity of these organisms.     

The functional significance of the microbial biomass in organic and conventionally managed soils

In order to achieve sustainability in managed ecosystems we must understand management impacts on soil processes and clarify the regulatory role of the microbial community on these processes. Crop rotation and organic management practices are thought to have positive impacts on the microbial biomass; however, the specific impacts of crop rotation organic management on soil microbial ecology are largely unknown. The effect of organic management on soil microbial ecology was investigated using soils collected from the Rodale Institute Research Center's long-term Farming Systems Trial (FST) experiment. The FST, begun in 1981, included a manured and a cover cropped organic rotation and a conventionally managed grain based rotation. Soil respiration rates and¹³C-isotope fate in a companion study suggest that the biomass characteristics of the FST treatment soils were different in November 1991. However, direct measurement of the microbial community at this time using Phospholipid Fatty Acid Analysis (PLFA) did not identify statistically significant treatment based differences in soil biomass characteristics. Variability among the PLFA profiles of treatment replicates was as great as variability between farming systems. Treatment based trends were observed among selected PLFAs, particularly those present in large amounts, that were consistent with indirect biomass and biomass-dependent measures. Overall, PLFA profiles, soil respiration rates and¹³C-cycling suggested that the organic cover cropped soil had the Largest and most heterogeneous microbial population while the biomass of the organic-manure amended soil was the least heterogeneous, and the most metabolically active. Present address: University of Illinois, 11025. Goodwin ave. Urbana, IL 61801, USA     

Bacterial diversity in Greenlandic soils as affected by potato cropping and inorganic versus organic fertilization

Arctic and Subarctic ecosystems will in the near future be exposed to severe environmental stresses due to global warming. For example, the microbial community structure and function may change as a result of increased temperatures. In Greenland, agriculture is carried out in the Subarctic regions with only limited pest management, despite the presence of plant pathogenic fungi. The microbial community composition in agricultural soils, which plays an important role for soil and plant health and for crop yield, may be affected by the use of different fertilizer treatments. Currently, only limited research has been performed on the effects of these treatments on bacterial communities in Arctic and Subarctic agricultural soils. The major objective of this study was to investigate the short-term impact of conventional (NPK) and organic (sheep manure supplemented with nitrogen) fertilizer treatments on bacterial diversity, nutrient composition and crop yield in two Greenlandic agricultural soils. An effect of fertilizer was found on soil and plant nutrient levels and on crop yields. Pyrosequencing of 16S rRNA gene sequences did not reveal any major changes in the overall bacterial community composition as a result of different fertilizer treatments, indicating a robust microbial community in these soils. In addition, differences in nutrient levels, crop yields and bacterial abundances were found between the two field sites and the two experimental growth seasons, which likely reflect differences in physical–chemical soil parameters.     

Long‐term farming systems and last crop sown shape the species and functional composition of the arable weed seed bank

Questions: The assembly of arable weed communities is the result of local filtering by agricultural management and crop competition. Therefore, soil seed banks can reflect the effects of long‐term cumulative field management and crop sequences on weed communities. Moreover, soil seed banks provide strong estimates of future weed problems but also of potential arable plant diversity and associated ecological functions. For this, we evaluated the effects of different long‐term farming systems under the same crop rotation sequence on the abundance, diversity and community assembly of weed seed bank, as well as on the functional diversity and composition. Location: DOK (biodynamic [D], bioorganic [O], conventional [K]) long‐term trial, Therwil, Switzerland. Methods: The effects of long‐term contrasted farming systems (i.e., biodynamic, organic, conventional, mineral and unfertilised systems) and last crop sown (i.e., wheat and maize) were evaluated on different indicators of species and functional diversity and composition of the weed soil seed bank. Results: The results showed significant influences of 40 years of contrasted farming systems on the diversity and composition of the seed bank, with higher diversities being found in unfertilised and organic farming systems, but also higher abundances than those found under conventional systems. Organic farming also allowed higher functional richness, dispersion and redundancy. Different farming systems triggered shifts in species and functional assemblies. Conclusions: The results highlight the importance of organic management for the maintenance of a diverse arable plant community and its functions. However, such results emphasise the need for appropriate yearly management to reduce the abundance of settled weediness and prevent affecting crop production. The farm management filtered community composition based on functional traits. Although the soil seed bank buffers the long‐term farming and crop sequence, the last crop sown and, thus, the yearly management were important determinants of seed bank composition.     

Distinct soil microbial diversity under long-term organic and conventional farming

Low-input agricultural systems aim at reducing the use of synthetic fertilizers and pesticides in order to improve sustainable production and ecosystem health. Despite the integral role of the soil microbiome in agricultural production, we still have a limited understanding of the complex response of microbial diversity to organic and conventional farming. Here we report on the structural response of the soil microbiome to more than two decades of different agricultural management in a long-term field experiment using a high-throughput pyrosequencing approach of bacterial and fungal ribosomal markers. Organic farming increased richness, decreased evenness, reduced dispersion and shifted the structure of the soil microbiota when compared with conventionally managed soils under exclusively mineral fertilization. This effect was largely attributed to the use and quality of organic fertilizers, as differences became smaller when conventionally managed soils under an integrated fertilization scheme were examined. The impact of the plant protection regime, characterized by moderate and targeted application of pesticides, was of subordinate importance. Systems not receiving manure harboured a dispersed and functionally versatile community characterized by presumably oligotrophic organisms adapted to nutrient-limited environments. Systems receiving organic fertilizer were characterized by specific microbial guilds known to be involved in degradation of complex organic compounds such as manure and compost. The throughput and resolution of the sequencing approach permitted to detect specific structural shifts at the level of individual microbial taxa that harbours a novel potential for managing the soil environment by means of promoting beneficial and suppressing detrimental organisms.     

Soil macrofauna diversity as a key element for building sustainable agriculture in Argentine Pampas

The agricultural activity in the Argentine Pampas, characterized by an important trend towards no-till soybean monocropping, has completely transformed the original Pampas landscape into a monotonous scenario with a continuous succession of farms of very low crop diversity. This process has led to soil physical, chemical and biological degradation in those systems. The increase of crop rotation rates in no-till and reduced tillage systems has been proposed as an alternative with reduced negative impact on soils in the context of conventional agriculture. On the other hand, extensive organic farming is also suggested as an alternative to high-input agriculture systems. In this article, we aim to explore how different variations of farming practices and systems impact soil macrofauna, along an edaphoclimatic gradient in the Pampas region. We studied the following systems: natural grassland (Gr) as indicator of the original community, extensive organic farming (Org), conventional agriculture with no-tillage and three crop rotation levels (Nt-R1, Nt-R2 and Nt-R3), and reduced tillage with two levels of crop rotation (Til and Til-R). We assessed soil macrofauna, with emphasis on earthworm, beetle and ant communities; and soil physical and chemical properties. Macrofaunal taxa composition was significantly affected by both management systems and edaphoclimatic conditions. The Gr community had pronounced differences from all the agricultural systems. The earthworm community from Gr had distinctive features from those of most agricultural systems, with Org and Nt-R3 being the most similar to Gr in native and exotic earthworm species, respectively. The beetle community in Org was the most different one, and the communities from the other systems did not show a pattern related to management. Ant community composition was not determined by management systems, but it was affected by edaphoclimatic conditions. All the studied macrofauna groups had a significant co-variation with soil physical and chemical properties, showing that both the characteristics of each soil relative to the geographic location and the effect of management on abiotic soil attributes have an important effect on soil macrofauna. This study confirms that biodiversity is being lost in Pampas soils, which implies a possible threat to the soil capacity to perform the processes that sustain soil functioning and hence plant productivity. Further considerations about the sustainability of the current agricultural model applied in the Argentine Pampas are needed.     

Land use and climatic factors structure regional patterns in soil microbial communities

Aim  Although patterns are emerging for macroorganisms, we have limited understanding of the factors determining soil microbial community composition and productivity at large spatial extents. The overall objective of this study was to discern the drivers of microbial community composition at the extent of biogeographical provinces and regions. We hypothesized that factors associated with land use and climate would drive soil microbial community composition and biomass.
Location  Great Basin Province, Desert Province and California Floristic Province, California, USA.
Methods  Using phospholipid fatty acid analysis, we compared microbial communities across eight land-use types sampled throughout the State of California, USA ( n = 1117).
Results  The main factor driving composition and microbial biomass was land-use type, especially as related to water availability and disturbance. Dry soils were more enriched in Gram-negative bacteria and fungi, and wetter soils were more enriched in Gram-positive, anaerobic and sulphate-reducing bacteria. Microbial biomass was lowest in ecosystems with the wettest and driest soils. Disturbed soils had less fungal and more Gram-positive bacterial biomass than wildland soils. However, some factors known to influence microbial communities, such as soil pH and specific plant taxa, were not important here.
Main conclusions  Distinct microbial communities were associated with land-use types and disturbance at the regional extent. Overall, soil water availability was an important determinant of soil microbial community composition. However, because of the inclusion of managed and irrigated agricultural ecosystems, the effect of precipitation was not significant. Effects of environmental and management factors, such as flooding, tillage and irrigation, suggest that agricultural management can have larger effects on soil microbial communities than elevation and precipitation gradients.     

Pyrosequencing Reveals the Influence of Organic and Conventional Farming Systems on Bacterial Communities

It has been debated how different farming systems influence the composition of soil bacterial communities, which are crucial for maintaining soil health. In this research, we applied high-throughput pyrosequencing of V1 to V3 regions of bacterial 16S rRNA genes to gain further insight into how organic and conventional farming systems and crop rotation influence bulk soil bacterial communities. A 2×2 factorial experiment consisted of two agriculture management systems (organic versus conventional) and two crop rotations (flax-oat-fababean-wheat versus flax-alfalfa-alfalfa-wheat) was conducted at the Glenlea Long-Term Crop Rotation and Management Station, which is Canada’s oldest organic-conventional management study field. Results revealed that there is a significant difference in the composition of bacterial genera between organic and conventional management systems but crop rotation was not a discriminator factor. Organic farming was associated with higher relative abundance of Proteobacteria, while Actinobacteria and Chloroflexi were more abundant in conventional farming. The dominant genera including Blastococcus, Microlunatus, Pseudonocardia, Solirubrobacter, Brevundimonas, Pseudomonas, and Stenotrophomonas exhibited significant variation between the organic and conventional farming systems. The relative abundance of bacterial communities at the phylum and class level was correlated to soil pH rather than other edaphic properties. In addition, it was found that Proteobacteria and Actinobacteria were more sensitive to pH variation.     

Cross-Site Soil Microbial Communities under Tillage Regimes: Fungistasis and Microbial Biomarkers

The exploitation of soil ecosystem services by agricultural management strategies requires knowledge of microbial communities in different management regimes. Crop cover by no-till management protects the soil surface, reducing the risk of erosion and nutrient leaching, but might increase straw residue-borne and soilborne plant-pathogenic fungi. A cross-site study of soil microbial communities and Fusarium fungistasis was conducted on six long-term agricultural fields with no-till and moldboard-plowed treatments. Microbial communities were studied at the topsoil surface (0 to 5 cm) and bottom (10 to 20 cm) by general bacterial and actinobacterial terminal restriction fragment length polymorphism (T-RFLP) and phospholipid fatty acid (PLFA) analyses. Fusarium culmorum soil fungistasis describing soil receptivity to plant-pathogenic fungi was explored by using the surface layer method. Soil depth had a significant impact on general bacterial as well as actinobacterial communities and PLFA profiles in no-till treatment, with a clear spatial distinction of communities (P < 0.05), whereas the depth-related separation of microbial communities was not observed in plowed fields. The fungal biomass was higher in no-till surface soil than in plowed soil (P < 0.07). Soil total microbial biomass and fungal biomass correlated with fungistasis (P < 0.02 for the sum of PLFAs; P < 0.001 for PLFA 18:2ω6). Our cross-site study demonstrated that agricultural management strategies can have a major impact on soil microbial community structures, indicating that it is possible to influence the soil processes with management decisions. The interactions between plant-pathogenic fungi and soil microbial communities are multifaceted, and a high level of fungistasis could be linked to the high microbial biomass in soil but not to the specific management strategy.     

养分管理对农田土壤微生物量的影响

土壤微生物与土壤质量、健康、植物的生产力和农业的可持续发展密切相关。任何对土壤中微生物的扰动都可能影响土壤的长期生产力,并可能产生严重后果。大量研究结果表明,肥料类型、施肥处理年限长短、施肥水平高低及施肥措施都会造成土壤成分的变化,进而影响土壤中微生物的生长以及繁殖。简要介绍了微生物量的几种测定方法,综述了各种养分管理措施对农田生态系统中土壤微生物量的影响,从而了解土壤微生物因人类对土壤的利用而发生的变化,以期为农业的可持续发展和生态环境的保护提供理论依据。     

Interactions between soil properties,agricultural management and cultivar type drive structural and functional adaptations of the wheat rhizosphere microbiome to drought

Rhizosphere microbial communities adapt their structural and functional compositions to water scarcity and have the potential to substantially mitigate drought stress of crops. To unlock this potential, it is crucial to understand community responses to drought in the complex interplay between soil properties, agricultural management and crop species. Two winter wheat cultivars, demanding and non-demanding, were exposed to drought stress in loamy Chernozem and sandy Luvisol soils under conventional or organic farming management. Structural and functional adaptations of the rhizosphere bacteria were assessed by 16S amplicon sequencing, the predicted abundance of drought-related functional genes in the bacterial community based on 16S amplicon sequences (Tax4Fun) and the activity potentials of extracellular enzymes involved in the carbon cycle. Bacterial community composition was strongly driven by drought and soil type. Under drought conditions, Gram-positive phyla became relatively more abundant, but either less or more diverse in Luvisol and Chernozem soil respectively. Enzyme activities and functional gene abundances related to carbon degradation were increased under drought in the rhizosphere of the demanding wheat cultivar in organic farming. We demonstrate that soil type, farming system and wheat cultivar each constitute important factors during the structural and/or functional adaptation of rhizobacterial communities in response to drought.     

Various forms of organic and inorganic P fertilizers did not negatively affect soil- and root-inhabiting AM fungi in a maize–soybean rotation system

Arbuscular mycorrhizal (AM) fungi are key components of most agricultural ecosystems. Therefore, understanding the impact of agricultural practices on their community structure is essential to improve nutrient mobilization and reduce plant stress in the field. The effects of five different organic or mineral sources of phosphorus (P) for a maize–soybean rotation system on AM fungal diversity in roots and soil were assessed over a 3-year period. Total DNA was extracted from root and soil samples collected at three different plant growth stages. An 18S rRNA gene fragment was amplified and taxa were detected and identified using denaturing gradient gel electrophoresis followed by sequencing. AM fungal biomass was estimated by fatty acid methyl ester analysis. Soil P fertility parameters were also monitored and analyzed for possible changes related with fertilization or growth stages. Seven AM fungal ribotypes were detected. Fertilization significantly modified soil P flux, but had barely any effect on AM fungi community structure or biomass. There was no difference in the AM fungal community between plant growth stages. Specific ribotypes could not be significantly associated to P treatment. Ribotypes were associated with root or soil samples with variable detection frequencies between seasons. AM fungal biomass remained stable throughout the growing seasons. This study demonstrated that roots and soil host distinct AM fungal communities and that these are very temporally stable. The influence of contrasting forms of P fertilizers was not significant over 3 years of crop rotation.     

Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China

The long-term application of excessive chemical fertilizers has resulted in the degeneration of soil quality parameters such as soil microbial biomass, communities, and nutrient content, which in turn affects crop health, productivity, and soil sustainable productivity. The objective of this study was to develop a rapid and efficient solution for rehabilitating degraded cropland soils by precisely quantifying soil quality parameters through the application of manure compost and bacteria fertilizers or its combination during maize growth. We investigated dynamic impacts on soil microbial count, biomass, basal respiration, community structure diversity, and enzyme activity using six different treatments [no fertilizer (CK), N fertilizer (N), N fertilizer + bacterial fertilizer (NB), manure compost (M), manure compost + bacterial fertilizer (MB), and bacterial fertilizer (B)] in the plowed layer (0–20 cm) of potted soil during various maize growth stages in a temperate cropland of eastern China. Denaturing gradient electrophoresis (DGGE) fingerprinting analysis showed that the structure and composition of bacterial and fungi communities in the six fertilizer treatments varied at different levels. The Shannon index of bacterial and fungi communities displayed the highest value in the MB treatments and the lowest in the N treatment at the maize mature stage. Changes in soil microorganism community structure and diversity after different fertilizer treatments resulted in different microbial properties. Adding manure compost significantly increased the amount of cultivable microorganisms and microbial biomass, thus enhancing soil respiration and enzyme activities (p<0.01), whereas N treatment showed the opposite results (p<0.01). However, B and NB treatments minimally increased the amount of cultivable microorganisms and microbial biomass, with no obvious influence on community structure and soil enzymes. Our findings indicate that the application of manure compost plus bacterial fertilizers can immediately improve the microbial community structure and diversity of degraded cropland soils.     

Effect of above-ground plant species on soil microbial community structure and its impact on suppression of Rhizoctonia solani AG3

The extent of soil microbial diversity is seen to be critical to the maintenance of soil health and quality. Different agricultural practices are able to affect soil microbial diversity and thus the level of suppressiveness of plant diseases. In a 4-year field experiment, we investigated the microbial diversity of soil under different agricultural regimes. We studied permanent grassland, grassland turned into arable land, long-term arable land and arable land turned into grassland. The diversity of microbial communities was described by using cultivation-based and cultivation-independent methods. Both types of methods revealed differences in the diversities of soil microbial communities between different treatments. The treatments with higher above-ground biodiversity generally maintained higher levels of microbial diversity. Moreover, a positive correlation between suppression of Rhizoctonia solani AG3 and microbial diversity was observed. Permanent (species-rich) grassland and grassland turned into maize stimulated higher microbial diversities and higher levels of suppressiveness of R. solani AG3 compared with the long-term arable land. Effects of agricultural practices on Bacillus and Pseudomonas communities were also observed and clear correlations between the levels of suppressiveness and the diversities of these bacterial groups were found. This study highlighted the importance of agricultural management regime for soil microbial community structure and diversity as well as the level of soil suppressiveness.     

Effects of cotton–maize rotation on soil microbiome structure

Verticillium wilt is a disastrous disease in cotton-growing regions in China. As a common management method, cotton rotation with cereal crops is used to minimize the loss caused by Verticillium dahliae. However, the correlation between soil microbiome and the control of Verticillium wilt under a crop rotation system is unclear. Therefore, three cropping systems (fallow, cotton continuous cropping, and cotton–maize rotation) were designed and applied for three generations under greenhouse conditions to investigate the different responses of the soil microbial community. The soil used in this study was taken from a long-term cotton continuous cropping field and inoculated with V. dahliae before use. Our results showed that the diversity of the soil bacterial community was increased under cotton–maize rotation, while the diversity of the fungal community was obviously decreased. Meanwhile, the structure and composition of the bacterial communities were similar even under the different cropping systems, but they differed in the soil fungal communities. Through microbial network interaction analysis, we found that Verticillium interacted with 17 bacterial genera, among which Terrabacter had the highest correlation with Verticillium. Furthermore, eight fungal and eight bacterial species were significantly correlated with V. dahliae. Collectively, this work aimed to study the interactions among V. dahliae, the soil microbiome, and plant hosts, and elucidate the relationship between crop rotation and soil microbiome, providing a new theoretical basis to screen the biological agents that may contribute to Verticillium wilt control.     

不同种植方式对绿洲农田土壤酶活性与微生物多样性的影响

研究了玉米连作10年、小麦连作8年 棉花连作10年、棉花连作15年和棉花6年 6年小麦/油葵轮作4种种植方式对土壤过氧化氢酶、蔗糖酶、芳基硫酸酯酶、脱氢酶和蛋白酶活性的影响,并分析了土壤细菌、真菌、氨氧化古菌与氨氧化细菌对北疆绿洲农田不同种植方式的响应.结果表明： 不同种植方式对土壤过氧化氢酶、芳基硫酸酯酶、脱氢酶和蛋白酶活性影响明显,但对蔗糖酶无显著影响;对氨氧化古菌多样性指数有显著影响,对土壤细菌、真菌和氨氧化细菌多样性指数无明显影响.土壤真菌和氨氧化细菌群落结构对不同种植方式的响应较细菌和氨氧化古菌敏感.长期棉花连作使绿洲农田土壤酶活性下降,微生物群落多样性降低,而轮作可提高土壤酶活性和微生物群落结构多样性.
     

Effect of organic and conventional farming on soil bacterial diversity of pecan tree (Carya illinoensis K. Kosh) orchard across two phenological stages

We described the bacterial diversity of walnut grove soils under organic and conventional farming. The bacterial communities of rhizospheric and nonrhizospheric soils of pecan tree (Carya illinoensis K. Koch) were compared considering two phenological stages (sprouting and ripening). Sixteen operational taxonomic units (OTUs) were identified significantly more abundant according to the plant development, only one according to the farming condition, and none according to the soil origin. The OTUs specificaly abundant according to plant development included Actinobateria (2) and Betaproteobacteria (1) related OTUs more abundant at the sprouting stage, while at the fruit ripening (FR) stage the more abundant OTUs were related to Actinobacteria (6), Alphaproteobacteria (6), and unclassified Bacteria (1). The Gaiellaceae OTU18 (Actinobacteria) was more abundant under conventional farming. Thus, our study revealed that the plant development stage was the main factor shaping the bacterial community structure, while less influence was noticed for the farming condition. The bacterial communities exhibited specific metabolic capacities, a large range of carbon sources being used at the FR stage. The identified OTUs specifically more abundant represent indicators providing useful information on soil condition, potential tools for the management of soil bacterial communities.     

Dynamics of plant nutrient uptake as affected by biopore-associated root growth in arable subsoil

Background and aims

Soil microbial communities influence nutrient cycling, chemistry and structure of soil, and plant productivity. In turn, agronomic practices such as fertilization and crop rotation alter soil physical and chemical properties and consequently soil microbiomes. Understanding the long-term effects of agronomic practices on soil microbiomes is essential for improving agronomic practices to optimize these microbial communities for agricultural sustainability. We examine the composition and substrate-utilization profiles of microbial communities at the Morrow Plots in Illinois.

Methods

Microbial community composition is assessed with 16S rRNA gene sequencing and subsequent bioinformatic analyses. Community- level substrate utilization is characterized with the BIOLOG EcoPlate.

Results

Fertilizer and rotation treatments significantly affected microbial community structure, while substrate utilization was affected by fertilizer, but not crop-rotation treatments. Differences in relative abundance and occurrence of bacterial taxa found in fertilizer treatments can explain the observed differences in community level substrate utilization.

Conclusion

Long-term fertilization and crop-rotation treatments affect soil microbial community composition and physiology, specifically through chronic nutrient limitation, long-term influx of microbes and organic matter via manure application, as well as through changes in soil chemistry. Relatively greater abundance of Koribacteraceae and Solibacterales taxa in soils might prove useful as indicators of soil degradation.