Communities In Agricultural Soils Research Articles

Impact of Anthracene Addition on Microbial Community Structure in Soil Microcosms from Contaminated and Uncontaminated Sites

Objective This paper aims to investigate the impact of anthracene addition on microbial community in agricultural soil irrigated with tap water or reclaimed wastewater. Methods The changes of microbial community were characterized by terminal restriction fragment length polymorphism in combination with 16S rRNA gene clone library analysis. Results A significant change in microbial community composition was observed during the biodegradation of anthracene, with dominantly enriched members from the genus Methylophilus. Conclusion This work might be useful for developing techniques for the isolation of novel putative PAH degrader.

Desert Farming Benefits from Microbial Potential in Arid Soils and Promotes Diversity and Plant Health

BackgroundTo convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known.Methodology/Principal FindingsWe studied the impact of long-term agriculture on desert soil in one of the most prominent examples for organic desert farming in Sekem (Egypt). Using a polyphasic methodological approach to analyse microbial communities in soil as well as associated with cultivated plants, drastic effects caused by 30 years of agriculture were detected. Analysing bacterial fingerprints, we found statistically significant differences between agricultural and native desert soil of about 60%. A pyrosequencing-based analysis of the 16S rRNA gene regions showed higher diversity in agricultural than in desert soil (Shannon diversity indices: 11.21/7.90), and displayed structural differences. The proportion of Firmicutes in field soil was significantly higher (37%) than in the desert (11%). Bacillus and Paenibacillus play the key role: they represented 96% of the antagonists towards phytopathogens, and identical 16S rRNA sequences in the amplicon library and for isolates were detected. The proportion of antagonistic strains was doubled in field in comparison to desert soil (21.6%/12.4%); disease-suppressive bacteria were especially enriched in plant roots. On the opposite, several extremophilic bacterial groups, e.g., Acidimicrobium, Rubellimicrobium and Deinococcus-Thermus, disappeared from soil after agricultural use. The N-fixing Herbaspirillum group only occurred in desert soil. Soil bacterial communities were strongly driven by the a-biotic factors water supply and pH.Conclusions/SignificanceAfter long-term farming, a drastic shift in the bacterial communities in desert soil was observed. Bacterial communities in agricultural soil showed a higher diversity and a better ecosystem function for plant health but a loss of extremophilic bacteria. Interestingly, we detected that indigenous desert microorganisms promoted plant health in desert agro-ecosystems.

Microbial Actvity and 13C/12C Ratio as Evidence of N-Hexadecane and N-Hexadecanoic Acid Biodegradation in Agricultural and Forest Soils

The dynamics of microbial degradation of exogenous contaminants, n-hexadecane and its primary microbial oxidized metabolite, n-hexadecanoic (palmitic) acid, was studied for topsoils, under agricultural management and beech forest on the basis the changes in O2 uptake, CO2 evolution and its associated microbial and non-microbial carbon isotopic signature, the respiratory quotient (RQ) and the priming effect (PE) of substrates. Soil microbial communities in agricultural soil responded to the n-hexadecane addition more rapidly compared to those of forest soil, with lag-periods of about 23 ± 10 and 68 ± 13 hours, respectively. Insignificant difference in the lag-period duration was detected for agricultural (tlag = 30 ± 13 h) and forest (tlag = 30 ± 14 h) soils treated with n-hexadecanoic (palmitic) acid. These results demonstrate that the soil microbiota differed in metabolic activities for using n-hexadecane as a reductive hydrocarbon and n-hexadecanoic acid as a partly oxidized hydrocarbon. The corresponding δ13C of respired CO2 after the addition of the hydrocarbon contaminants to soils indicates a shift in microbial activity towards the consumption of exogenous substrates with a more complete degradation of n-hexadecane in the agricultural soil, for which some initial contents of hydrocarbons are inherent. It was reflected in the carbon isotope signature of microbial biomass. It is supposed that the observed deviation of RQ from theoretically calculated value under microbial substrate mineralization is determined by difference in the time (Δti) of registration of CO2 production and O2 consumption. Positive priming effect (PE) of n-hexadecane and negative PE of n-hexadecanoic (palmitic) acid were detected in agricultural and forest soils. It is suggested that positive PE of n-hexadecane is conditioned by the induction of microbial enzymes that perform hydroxylation/oxygenation of stable SOM compounds mineralized by soil microbiota to CO2. The microbial metabolism coupled with oxidative decarboxylation of n-hexadecanoic acid is considered as one of the most probable causes of the revealed negative PE value.

Application of molecular ecological techniques to study microbial communities in agricultural soils

Application of molecular ecological techniques to study microbial communities in agricultural soils

The establishment of culture-independent molecular biological methods for analyses of microbial community in agricultural soils(JSSPN Progress Awards)

The establishment of culture-independent molecular biological methods for analyses of microbial community in agricultural soils(JSSPN Progress Awards)

Molecular diversity of fungal communities in agricultural soils from Lower Austria.

A culture-independent survey of fungal diversity in four arable soils and one grassland in Lower Austria was conducted by RFLP and sequence analysis of clone libraries of the partial ITS/LSU-region. All soils were dominated by the ascomycetous orders Sordariales, Hypocreales and Helotiales, taxa that are known from traditional cultivation approaches to occur in agricultural soils. The most abundant genus in the investigated soils was Tetracladium, a hyphomycete which has been described as occurring predominantly in aquatic habitats, but was also found in agricultural soils. Additionally, soil clone group I (SCGI), a subphylum at the base of the Ascomycota with so far no cultivated members, was identified at high frequency in the grassland soil but was below detection limit in the four arable fields. In addition to this striking difference, general fungal community parameters like richness, diversity and evenness were similar between cropland and grassland soils. The presented data provide a fungal community inventory of agricultural soils and reveal the most prominent species.

Positive effects of organic farming on below‐ground mutualists: large‐scale comparison of mycorrhizal fungal communities in agricultural soils

*The impact of various agricultural practices on soil biodiversity and, in particular, on arbuscular mycorrhizal fungi (AMF), is still poorly understood, although AMF can provide benefit to plants and ecosystems. Here, we tested whether organic farming enhances AMF diversity and whether AMF communities from organically managed fields are more similar to those of species-rich grasslands or conventionally managed fields. *To address this issue, the AMF community composition was assessed in 26 arable fields (13 pairs of organically and conventionally managed fields) and five semi-natural grasslands, all on sandy soil. Terminal restriction fragment length polymorphism community fingerprinting was used to characterize AMF community composition. *The average number of AMF taxa was highest in grasslands (8.8), intermediate in organically managed fields (6.4) and significantly lower in conventionally managed fields (3.9). Moreover, AMF richness increased significantly with the time since conversion to organic agriculture. AMF communities of organically managed fields were also more similar to those of natural grasslands when compared with those under conventional management, and were less uniform than their conventional counterparts, as expressed by higher beta-diversity (between-site diversity). *We suggest that organic management in agro-ecosystems contributes to the restoration and maintenance of these important below-ground mutualists.

Influence of commercial inoculation with Glomus intraradices on the structure and functioning of an AM fungal community from an agricultural site

The use of commercial arbuscular mycorrhizal (AM) inoculants is growing. However, we know little about how resident AM communities respond to inoculations under different soil management conditions. The objective of this study was to simulate the application of a commercial AM fungal inoculant of Glomus intraradices to soil to determine whether the structure and functioning of that soil’s resident AM community would be affected. The effects of inoculation were investigated over time under disturbed or undisturbed soil conditions. We predicted that the introduction of an infective AM fungus, such as G. intraradices, would have greater consequences in disturbed soil. Using a combination of molecular (terminal restriction length polymorphism analysis based on the large subunit of the rRNA gene) and classical methods (AM fungal root colonization and P nutrition) we found that, contrary to our prediction, adding inoculant to soil containing a resident AM fungal community does not necessarily have an impact on the structure of that community either under disturbed or undisturbed conditions. However, we found evidence of positive effects of inoculation on plant nutrition under disturbed conditions, suggesting that the inoculant interacted, directly or indirectly, with the resident AM fungi. The inoculant significantly improved the P content of the host but only in presence of the resident AM fungal community. In contrast to inoculation, soil disturbance had a significant negative impact on species richness of AM fungi and influenced the AM fungal community composition as well as its functioning. Thus, we conclude that soil disturbance may under certain conditions have greater consequences for the structure of resident AM fungal communities in agricultural soils than commercial AM fungal inoculations with G. intraradices.

Habitat selective factors influencing the structural composition and functional capacity of microbial communities in agricultural soils

Key physicochemical factors associated with microbial community composition and functions in Australian agricultural soils were identified. Soils from seven field sites, with varying long-term agricultural management regimes, were characterised physicochemically, on the basis of their bacterial and fungal community structures (using PCR-DGGE), and by assessing potential catabolic functions (MicroResp™). Soil type, rather than agricultural management practice, was the key determinant of microbial community structure and catabolic function ( P<0.05). Following multivariate analysis, soil pH was identified as the key habitat-selective physicochemical soil property associated with variation in biological diversity and profiles of organic substrate utilisation. In particular, the capacity of soils to catabolise different C-substrates was closely correlated ( ρ=0.604, P=0.001) to pH. With decreasing pH, the catabolism of common low molecular weight organic compounds (especially cysteine and aspartic acid) declined, however catabolism of two others (lysine and arginine) increased. Shifts in the capacity of soil microbiota to cycle common organic compounds have implications for overall geochemical cycling of C and N in acidifying soils. The genetic structure of the bacterial communities in soil strongly correlated with pH ( ρ=0.722; P=0.001) and that of soil fungi with pH and % sand ( ρ=0.323; P=0.006). Catabolic function was more closely associated with the structure of the bacterial than fungal communities. This work has shown that soil pH is a primary driver of microbial diversity and function in soil. Agricultural management practices thereby act to selectively shift populations and functions against this background.

Suppressive service of the soil food web: Effects of environmental management

Soil food webs perform the important ecosystem services necessary to maintain both agricultural productivity and ecosystem health. Higher trophic levels in soil food webs can play a role suppressing plant parasites and affecting nutrient dynamics by modifying abundance of intermediate consumers. Natural and agricultural landscapes were sampled to compare soil faunal structure. Top-down soil suppressiveness of a parasitic nematode, Meloidogyne incognita, was determined in laboratory assay. Five treatments, including two nitrogen fertilizers, two herbicides and simulated tillage were established in experimental microcosms to evaluate the effects of simulated agricultural practices on top-down suppressiveness. Soil food web indices, based on the composition of the nematode fauna, were calculated to infer soil food web condition. Long and complex soil food webs in natural areas, with more trophic links and abundant predatory nematodes, effectively suppressed plant–parasite populations, while disturbed communities in agricultural soils did not. Soil suppressiveness was related to the ratio of predators to prey and to the prevalence of omnivore and predator species. Agricultural management led to a reduction in the suppressive capacity of the soil food web. Abundance of predatory nematodes was related to soil NH4+, probably due to excretory products of nematodes and other organisms grazing on microbes. Soil suppressiveness, soil food web dynamics and agricultural management are strongly inter-related.

Microbial community changes during humification of 14C‐labelled maize straw in heat‐treated and native Orthic Luvisol

SummaryThe microbial communities in agricultural soils are responsible for nutrient cycling and thus for maintaining soil fertility. However, there is still a considerable lack of knowledge on anthropogenic impacts on soils, their microflora, and the associated nutrient cycles. In this microcosm study, microorganisms involved in the conversion of crop residues were investigated by means of classical microbiological and molecular methods such as denaturing gradient gel electrophoresis (DGGE) of PCR (polymerase chain reaction) amplified 16S rRNA genes. 14C‐labelled maize straw was humified by the naturally occurring microflora in native and in ashed soils, from which organic carbon was removed by heating at 600°C. The humic acids synthesized in the microcosms served as indicators of the humification process and were analysed by 13C‐NMR spectroscopy. Ashed, autoclaved and native soil exhibited similar microbial and physicochemical dynamics after inoculation with a soil suspension. Bacterial counts and DGGE analyses showed that in the first few weeks a small number of rapidly growing r‐strategists were principally responsible for the conversion of maize straw. As the incubation continued, the bacterial diversity increased as well as the fungal biomass. 13C‐NMR spectroscopy of 26‐week old soil extracts revealed that structures typical of humic substances also evolved from the plant material.

Ammonia-oxidizing communities in agricultural soil incubated with organic waste residues

The impact of organic compounds present in different kinds of organic fertilizers, i.e., anaerobically digested household waste, composted organic household waste, swine manure, and cow manure, on microbial communities in arable soil was investigated using microcosms. Soil was amended with dried residues or organic extracts of the residues and incubated for 12 weeks at 25°C. The microbial community composition was investigated by phospholipid fatty acid (PLFA) analysis, and the community of ammonia-oxidizing bacteria (AOB) was assessed by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA fragments, followed by sequencing. All dried residues increased the AOB activity, determined as potential ammonia oxidation, whereas the organic extracts from the thermophilically digested waste and the swine manure caused a decreased potential activity. However, no differences in the DGGE banding patterns were detected, and the same AOB sequences were present in all samples treated with the residue extracts. Moreover, the PLFA composition showed that none of the residue additions affected the overall microbial community structure in the soil. We conclude that the AOB community composition was not affected by the organic compounds in the fertilizers, although the activity in some cases was.

Effects of copper amendment on the bacterial community in agricultural soil analyzed by the T-RFLP technique

The impact of copper amendment on the bacterial community in agricultural soil was investigated by a 2-year field experiment complemented by short-term microcosm studies. In the field, the amendments led to total copper contents that were close to the safety limits laid down by European authorities. In parallel, bioavailable copper was determined with a copper-specific bioluminescent Pseudomonas reporter strain. The amounts of total Cu as well as of bioavailable Cu in the field declined throughout the experiment. Bacterial community structure was examined by terminal restriction fragment length polymorphism (T-RFLP) analysis of community DNA amplified with primers specific for 16S rDNA from the Bacteria domain, the Rhizobium- Agrobacterium group and the Cytophaga group. Similarity analysis of T-RFLP profiles from field samples demonstrated an impact of copper at the domain level and within the Rhizobium- Agrobacterium group. Comparable Cu effects were observed for microcosms, but in addition an impact on community structure within the Cytophaga group was observed.

Long-term effects of mineral versus organic fertilizers on activity and structure of the methanotrophic community in agricultural soils.

Agricultural practices, such as mineral nitrogen fertilization, have an impact on the soil's ability to oxidize methane, but little is known about the shifts in the methanotrophic community composition associated with these practices. Therefore, the long-term effect of both mineral (NH4NO3) and organic (manure and GFT-compost) fertilizer applications on the soil methanotrophic community activity and structure were investigated. Both high and low affinity methane oxidation rates were lower in the soil treated with mineral fertilizer compared to the other soils. An enhanced nitrate concentration was observed in the mineral fertilized soil but nitrate did not show a direct affect on the high affinity methane oxidation. In contrast, the low affinity methane oxidation was slowed down by increased nitrate concentrations, which suggests a direct effect of nitrate on low affinity methane oxidation. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments specific for methanotrophs revealed a distinct community between the mineral and organic fertilized soils as extra Type I methanotrophic bands (phylotypes) became visible in the organic fertilized soils. These phylotypes were not visible in the patterns of the added organic fertilizers suggesting an indirect effect of the organic fertilizers on the methanotrophic community. Additionally, a molecular analysis was performed after the low affinity methane oxidation test. The enhanced methane concentrations used in the test enriched certain low affinity methanotrophs in the organic fertilized soils but not in the mineral fertilized soil. Supporting the molecular and functional observations, fatty acids characteristic for methanotrophs were less abundant in the soil treated with mineral fertilizer compared to the soil treated with compost. In conclusion, the function and molecular and chemical composition of the methanotrophic community are all altered in soil fertilized with mineral fertilizer.