Function Of Soil Microorganisms Research Articles

Effects of grassland afforestation on structure and function of soil bacterial and fungal communities

Grassland afforestation strongly influences the structure and function of soil microorganisms. Yet the mechanisms of how afforestation could simultaneously alter both the soil fungal and bacterial communities and its implications for ecosystem management are poorly understood, especially in nitrogen-limited ecosystems. Using high-throughput sequencing of 16S rRNA and ITS rRNA genes, the present study investigated the changes in soil properties and soil microorganisms after afforestation of natural grasslands with Chinese pine (Pinus tabuliformis) on the Loess Plateau in China. Results showed that soil bacterial diversity had no significant differences among the grassland (GL), forest–grassland transition zone (TZ), and forestland (FL), while soil fungal diversity in the GL was significantly higher than that in the FL and TZ (P < 0.05). The proportion of shared OTUs in the soil bacterial community was higher than that in the soil fungal community among the three land use types. The dominant bacterial phylum shifted from Proteobacteria to Actinobacteria, while the dominant fungal phylum shifted from Ascomycota to Basidiomycota after the GL conversion to the FL. The functional groups of ECM fungi increased significantly while biotrophic fungi decreased significantly after grassland afforestation. Both the soil bacterial and fungal communities in the TZ showed great similarity with those in the FL. In addition, among all examined soil properties, soil nitrogen (N) showed a more significant effect on the soil microbial communities. The reduction of soil N after grassland afforestation resulted in both the structure and function changes in soil microbial communities. Our results demonstrated simultaneously differential changes in the composition and diversity of both soil bacterial and fungal communities after afforestation from grasslands to planted forests.

Blame It on the Metabolite: 3,5-Dichloroaniline Rather than the Parent Compound Is Responsible for the Decreasing Diversity and Function of Soil Microorganisms.

Pesticides are key stressors of soil microorganisms with reciprocal effects on ecosystem functioning. These effects have been mainly attributed to the parent compounds, while the impact of their transformation products (TPs) has been largely overlooked. We assessed in a meadow soil (soil A) the transformation of iprodione and its toxicity in relation to (i) the abundance of functional microbial groups, (ii) the activity of key microbial enzymes, and (iii) the diversity of bacteria, fungi, and ammonia-oxidizing microorganisms (AOM) using amplicon sequencing. 3,5-Dichloroaniline (3,5-DCA), the main iprodione TP, was identified as a key explanatory factor for the persistent reduction in enzymatic activities and potential nitrification (PN) and for the observed structural changes in the bacterial and fungal communities. The abundances of certain bacterial (Actinobacteria, Hyphomicrobiaceae, Ilumatobacter, and Solirubrobacter) and fungal (Pichiaceae) groups were negatively correlated with 3,5-DCA. A subsequent study in a fallow agricultural soil (soil B) showed limited formation of 3,5-DCA, which concurred with the lack of effects on nitrification. Direct 3,5-DCA application in soil B induced a dose-dependent reduction of PN and NO3--N, which recovered with time. In vitro assays with terrestrial AOM verified the greater toxicity of 3,5-DCA over iprodione. "Candidatus Nitrosotalea sinensis" Nd2 was the most sensitive AOM to both compounds. Our findings build on previous evidence on the sensitivity of AOM to pesticides, reinforcing their potential utilization as indicators of the soil microbial toxicity of pesticides in pesticide environmental risk analysis and stressing the need to consider the contribution of TPs in the toxicity of pesticides on the soil microbial community.IMPORTANCE Pesticide toxicity on soil microorganisms is an emerging issue in pesticide risk assessment, dictated by the pivotal role of soil microorganisms in ecosystem services. However, the focus has traditionally been on parent compounds, while transformation products (TPs) are largely overlooked. We tested the hypothesis that TPs can be major contributors to the soil microbial toxicity of pesticides using iprodione and its main TP, 3,5-dichloroaniline, as model compounds. We demonstrated, by measuring functional and structural endpoints, that 3,5-dichloroaniline and not iprodione was associated with adverse effects on soil microorganisms, with nitrification being mostly affected. Pioneering in vitro assays with relevant ammonia-oxidizing bacteria and archaea verified the greater toxicity of 3,5-dichloroaniline. Our findings are expected to advance environmental risk assessment, highlighting the potential of ammonia-oxidizing microorganisms as indicators of the soil microbial toxicity of pesticides and stressing the need to consider the contribution of TPs to pesticide soil microbial toxicity.

Monitoring Soil Bacteria with Community-Level Physiological Profiles Using Biolog™ ECO-Plates in the Republic of Tatarstan (Russia)

Conservation of soil fertility is one of the most important tasks of the present time. As microorganisms are among the key factors in forming soil fertility, monitoring their state in natural and anthropogenically changed soils is an important component of compulsory environmental monitoring. Modern methods make it possible to evaluate the diversity and the functions of soil microorganisms, however, unfortunately, not all the soils are analyzed with their help up to the present moment. The present investigation is aimed to evaluate the functional diversity of five natural soil samples in the Republic of Tatarstan (belonging to sod-podzol, sod-carbonate, alluvial, and gray types) using the method of Biolog EcoPlate according to the index of average well color development, alpha-biodiversiry Shannon index (H), amount of substrates consumed ®, and strategy of consumption of various carbon substrate groups. It was shown that the highest AWCD index was found in sample No 3 – alluvial soil type (3.159±0.460), the lowest one – in sample No 5 – gray soil type (0.572±0.230). Correlation of biological activity of microorganisms with organic matter content in soil was shown.

NATURAL ANTIBIOTIC RESISTANCE GENES IN SOIL BACTERIA AND INFLUENCE OF ORGANIC FERTILISERS ON THEIR PREVALENCE AND HORIZONTAL TRANSFER

All natural antibiotics available to modern medicine are products of soil-dwelling bacteria and fungi. In addition, all resistance genes which are being detected in human pathogens existed in soil bacteria even before antibiotics were discovered and brought into use. However, the concentrations of natural antibiotics in soil are usually subinhibitory – insuffi cient for the selection of resistant subpopulations of microorganisms. The consumption of organic fertilisers for agricultural soil amendment increases proportionally to the consumers’ growing demand for organically produced food. Manure originating from industrial pig, cattle and poultry farms is not only the source of nutrients which stimulate the vital functions of soil microorganisms, but also of antibiotics and bacteria harbouring various resistance mechanisms. The application of organic fertilizer leads to disruption of the natural balance between bacterial communities in the soil through several mechanisms, and infl uences the increase in the prevalence of resistance genes and promotes their horizontal transfer. Whether as-yet-unknown resistance genes in soil bacteria may pose threat to human health if transferred from commensal bacteria in the environment to pathogen species, or migrate to clinical settings via food chain or in some other possible route - remains an open question.

Effects of intercropping on soil CO2 and N2O emissions from upland: A review.

Greenhouse gases (GHGs) emission from arable field is a hot topic recently, adopting appropriate cropping systems is an effective way to reduce GHGs emission. This paper reviewed the impacts and mechanisms of intercropping on soil CO2 and N2O emissions in upland field. Rational intercropping systems could increase soil organic carbon (SOC), promote the transformation of straw to SOC, slow down mineralization rate of SOC, and hence reduce soil CO2 emissions. The Poaceae intercropping with legume could maintain the stability of yield while reducing synthetic N inputs, formation of inorganic N by residue decomposition and soil mineral N, and further reducing soil N2O emission. In addition, crop interactions in intercropping system and filed microclimate were important factors on GHGs emission as well. It is necessary to extent the period of researches in field GHGs emission in order to fully understand the underlying mechanisms of GHGs emission in farm land, especially the function of soil microorganisms at molecular level. It would provide theoretical knowledge in building environment-friendly agricultural system in the future.

Impact of an invasive nitrogen-fixing tree on arbuscular mycorrhizal fungi and the development of native species.

Arbuscular mycorrhizal fungi (AMF) are obligate soil biotrophs that establish intimate relationships with 80 % of terrestrial plant families. Arbuscular mycorrhizal fungi obtain carbon from host plants and contribute to the acquisition of mineral nutrients, mainly phosphorus. The presence of invasive plants has been identified as a soil disturbance factor, often conditioning the structure and function of soil microorganisms. Despite the investigation of many aspects related to the invasion ofAcacia dealbata, the effect produced on the structure of AMF communities has never been assessed. We hypothesize thatA. dealbatamodifies the structure of AMF community, influencing the establishment and growth of plants that are dependent on these mutualisms. To validate our hypothesis, we carried out denaturing gradient gel electrophoresis (DGGE) analysis and also grew plants ofPlantago lanceolatain pots using roots of native shrublands or fromA. dealbata, as inoculum of AMF. Cluster analyses from DGGE indicated an alteration in the structure of AMF communities in invaded soils. After 15 weeks, we found that plants grown in pots containing native roots presented higher stem and root growth and also produced higher biomass in comparison with plants grown withA. dealbatainoculum. Furthermore, plants that presented the highest biomass and growth exhibited the maximum mycorrhizal colonization and phosphorus content. Moreover, fluorescence measurements indicated that plants grown withA. dealbatainoculum even presented higher photosynthetic damage. Our results indicate that the presence of the invaderA. dealbatamodify the composition of the arbuscular fungal community, conditioning the establishment of native plants.

How do soil animals bring out the functioning of soil microorganisms?

How do soil animals bring out the functioning of soil microorganisms?

Microscale distribution and function of soil microorganisms in the interface between rhizosphere and detritusphere

The rhizosphere and the detritusphere are hot spots of microbial activity, but little is known about the interface between rhizosphere and detritusphere. We used a three-compartment pot design to study microbial community structure and enzyme activity in this interface. All three compartments were filled with soil from a long-term field trial. The two outer compartments were planted with maize (root compartment) or amended with mature wheat shoot residues from a free air CO2 enrichment experiment (residue compartment) and were separated by a 50 μm mesh from the inner compartment. Soil, residues and maize differed in 13C signature (δ13C soil −26.5‰, maize roots −14.1‰ and wheat residues −44.1‰) which allowed tracking of root- and residue-derived C into microbial phospholipid fatty acids (PLFA). The abundance of bacterial and fungal PLFAs showed clear gradients with highest abundance in the first 1–2 mm of the root and residue compartment, and generally higher values in the vicinity of the residue compartment. The δ13C of the PLFAs indicated that soil microorganisms incorporated more carbon from the residues than from the rhizodeposits and that the microbial use of wheat residue carbon was restricted to 1 mm from the residue compartment. Carbon incorporation into soil microorganisms in the interface was accompanied by strong microbial N immobilisation evident from the depletion of inorganic N in the rhizosphere and detritusphere. Extracellular enzyme activities involved in the degradation of organic C, N and P compounds (β-glucosidase, xylosidase, acid phosphatase and leucin peptidase) did not show distinct gradients in rhizosphere or detritusphere. Our microscale study showed that rhizosphere and detritusphere differentially influenced microbial C cycling and that the zone of influence depended on the parameter assessed. These results are highly relevant for defining the size of different microbial hot spots and understanding microbial ecology in soils.

Land-use intensity modifies spatial distribution and function of soil microorganisms in grasslands

Abstract The aim of the present study was to investigate whether land-use intensity (LUI) contributes to spatial variation in microbial abundance and function in grassland ecosystems. At one time point, three sites at low (unfertilized pastures), at intermediate (fertilized mown pastures) and at high (fertilized mown meadows) LUIs were selected in southern Germany. Within each of these nine grassland sites, 54 soil samples (0–10 cm) were taken in a 10 m × 10 m area in spring. Plot-scale spatial dependence and autocorrelation of soil biogeochemical properties, microbial biomass and enzymes involved in C-, N- and P-cycling were analyzed. Applying geostatistics (exponential or spherical model) revealed that most chemical and microbiological properties showed at least a moderate spatial autocorrelation. Chemical soil properties (e.g. C org , N t , pH) were characterized by practical ranges (pRange) of between 1 and 14 m, whereas soil microbiological properties showed a greater variation of pRanges, providing evidence of spatial heterogeneity at multiple scales. The expected decrease in small-scale spatial heterogeneity in high LUI could not be confirmed for microbiological soil properties, because sampling in early spring might have reduced the influence of growing plants and fertilization. However, microbial biomass carbon was significantly greater in high LUIs, indicating that the benefit to soil microbial populations from the long-term increase in substrate and nutrient availability in fertilized grasslands is independent from factors affecting spatial structures in the short-term.

Abundance and activity of nitrate reducers in an arable soil are more affected by temporal variation and soil depth than by elevated atmospheric [CO2

Elevated atmospheric carbon dioxide concentrations ([CO(2) ]) might change the abundance and the function of soil microorganisms in the depth profile of agricultural soils by plant-mediated reactions. The seasonal pattern of abundance and activity of nitrate-reducing bacteria was studied in a Mini-FACE experiment planted with oilseed rape (Brassica napus). Three depths (0-10, 10-20 and 20-30 cm) were sampled. Analyses of the abundances of total (16S rRNA gene) and nitrate-reducing bacteria (narG, napA) revealed strong influences of sampling date and depth, but no [CO(2)] effects. Abundance and activity of nitrate reducers were higher in the top soil layer and decreased with depth but were not related to extractable amounts of nitrogen and carbon in soil. Dry periods reduced abundances of total and nitrate-reducing bacteria, whereas the potential activity of the nitrate reductase enzyme was not affected. Enzyme activity was only weakly correlated to the abundance of nitrate-reducing bacteria but was related to NH(4) (+) and NO(3) (-) concentrations. Our results suggest that in contrast to the observed pronounced seasonal changes, the elevation of atmospheric [CO(2) ] has only a marginal impact on nitrate reducers in the investigated arable ecosystem.

Available Organic Soil Phosphorus Has an Important Influence on Microbial Community Composition

Soil acidity can have a potent influence on soil microbial composition and function, but it remains unclear if this influence is a direct response to the concentration of H+or an indirect response caused by the influence of pH on other soil chemical properties. We hypothesized that the composition and function of soil microorganisms would shift in response to decreases in the availability of inorganic P caused by mobilized Al. We tested this hypothesis at Dysart Woods, a mosaic of old growth and second growth mixed, mesophytic forest in eastern Ohio. We evaluated microbial community composition (phospholipid fatty acid [PLFA] analysis) and function (extracellular enzyme activity) in the context of P availability and common metrics of soil fertility. We observed a threshold response where available organic P (Po, i.e., bicarbonate‐extracted, molybdate‐unreactive P) dominated (∼80%) the availability of total available P when mobilized Al was present (&gt;0.1 cmolckg−1), but when Al was immobilized, available inorganic P (Pi, i.e., bicarbonate‐extracted, molybdate‐reactive P) content was significantly greater (∼50%). Available Posignificantly correlated (r= 0.54) with acid phosphatase activity. Using nonmetric multidimensional scaling, we observed that PLFA composition ordination was significant along a gradient of soil pH and available PoBecause the composition and function of the microbial community changes due to available Po, results suggest that microbial communities in acidic forest soils are functionally P limited. The availability of Podid not influence the microbial biomass, however, indicating that the microbial community compensates for the apparent P limitation by altering its composition.

Assessment of the bacterial diversity in soils: Evolution of approaches and methods

This review analyzes the publications of Russian and foreign microbiologists presenting new approaches and methods for assessing the bacterial diversity of soils in the last twenty years. Using the example of peat soils, it is shown how the concepts of the diversity of the bacterial communities changed in conformity with the evolution of the analytical methods—from the traditional cultural to the molecular-biological ones. The data on the new phylotypes, genera, and species of bacteria adapted to growth in the acid medium and low temperatures characteristic of bog ecosystems are presented. Presently, one of the principal problems of soil microbiology is the necessity of the transfer from the databases on the microbial diversity constructed on the basis of molecular-biological methods to the analysis of the ecological functions of soil microorganisms. The prospects of the ecological evaluation of the bacterial diversity in soils based on the integration of different methods are discussed.

Soil management modifies micro‐scale abundance and function of soil microorganisms in a Mediterranean ecosystem

SummaryThe present study tests whether soil management (tillage and fertilizer) modified the small‐scale abundance and function of soil microorganisms in response to changes in organic matter quantity and quality. The experimental field, located in the coastal hills of Marche (central Italy), was planted in rotation with Triticum durum in winter and Zea mais in summer. Soil samples were collected in the maize‐field soil, in conventional and no‐tillage (NT) systems, and in fertilized and unfertilized soil. We analysed total organic C (TOC), total nitrogen (TN) microbial biomass C (MBC), enzymes involved in C‐ (β‐glucosidase, α‐glucosidase, β‐cellobiohydrolase, β‐xylosidase), N‐ (leucine‐aminopeptidase and N‐acetyl‐β‐glucosaminidase), P‐ (acid phosphatase) and S‐cycling (arylsulphatase), as well as functional diversity in the bulk soil, coarse sand, fine sand, silt and clay fractions. Micro‐scale investigations revealed great microbial abundance in smaller fractions because of protection offered by microaggregates, whereas the distribution of enzymes reflected the availability of their corresponding substrates. No‐tillage treatment significantly increased organic input, mainly in the coarser fractions, enhancing enzyme activities and the functional diversity of the microbial community. This effect was even larger in the absence of fertilizer. At the particle‐size level of resolution, adding fertilizer stimulated nutrient cycling. Our results confirmed the hypothesis that no‐tillage enlarges the content of particulate organic matter in the coarse sand fraction and stimulates microbial decomposition. In the smaller fractions the enlarged microbial pool and increased soil organic matter with small C/N ratio under NT confirm that this management practice is effective in increasing soil C sequestration capacity.

Mechanisms of solute transport affect small‐scale abundance and function of soil microorganisms in the detritusphere

SummaryIn the detritusphere, particulate organic matter offers new sites for microorganisms, whereas soluble substrates are transported into the adjacent soil. We investigated how mechanisms of solute transport affect microbial abundance and function in the detritusphere. In a first experiment, transport was restricted to diffusion, whereas in a second experiment it was dominated by convection. Two soil moisture contents were established in each experiment. When diffusion was the exclusive transport mechanism, the addition of maize litter induced distinct gradients in enzyme activities, soil organic C content and microbial biomass to a depth of 1.5–2.8 mm. Convection enlarged these gradients to 2.5–3.0 mm. The moisture regime modified the temporal pattern of diffusive C transport, microbial growth and enzyme release by inducing faster transport at large water contents. Convective transport seemed to be unaffected by soil moisture content. Using a convective‐diffusive transport model with first‐order decay, it was possible to simulate the observed activity profiles. The results indicate that the spatial dimension of the detritusphere is governed by the ratio between decay rate of available substrates and transport rate. Bacteria and fungi showed differing utilization strategies as revealed by coupling phospholipid fatty acid (PLFA) analysis with stable isotope techniques. Fungi assimilated C directly in the litter, whereas bacteria took up the substrates in the soil and therefore depended more on transport processes than fungi. Our results demonstrate the impact of physicochemical conditions on the abundance and function of microorganisms in the detritusphere. Furthermore, the combination of enzymatic measurements and mathematical transport modelling may offer a new way to measure substrate decay rates in soil.

Effect of Mucor alternans on the persistence of DDT and Dieldrin in culture and in soil.

Several fungi were isolated from an agricultural loam soil and tested for their capacity to degrade the insecticides DDT or dieldrin. It was found that Mucor alter nans van Tieghen in shake cultures partially degraded DDT within 2 to 4 days into 3 hexane-soluble and 2 water-soluble metabolites. None of these compounds had R1 valutes that were identical to those observed with DDD (TDE), DDE (1,1-dichloro-2,2-bis (p-chlorophenyl) ethylene), DDA (bis-(p-chlorophenyl) acetic acid), DBP (4,4´-dichlorobenzophenone), dicofol, and 1,1-bis (p-chloropbenyl) ethane. After application of C14-DDT, 42% of the totally recovered radioactivity was represented by the 2 water-soluble metabolites. Some indication of dieldrin breakdown by the fungus was evident, but no metabolites could be isolated. Degradation of both DDT and dieldrin occurred only with live fungi mycelia, while the insecticides were passively absorbed to dead mycelial controls. After the addition of M. alternans spores to a DDT- or dieldrin-contaminated agricultural loam soil, the insecticide degrading capacity of the fungus was no longer evident. This result was rather disappointing since a need exists to be able to degrade persistent pesticides in nature with soil microorganisms. Since DDE was only found in nonautoclaved soils, its formation from DDT was a function of soil microorganisms.