Microorganisms In Agricultural Soils Research Articles

Reveal molecular mechanism on the effects of silver nanoparticles on nitrogen transformation and related functional microorganisms in an agricultural soil

Silver nanoparticles (AgNPs) are widely present in aquatic and soil environment, raising significant concerns about their impacts on creatures in ecosystem. While the toxicity of AgNPs on microorganisms has been reported, their effects on biogeochemical processes and specific functional microorganisms remain relatively unexplored. In this study, a 28-day microcosmic experiment was conducted to investigate the dose-dependent effects of AgNPs (10 mg and 100 mg Ag kg−1 soil) on nitrogen transformation and functional microorganisms in agricultural soils. The molecular mechanisms were uncovered by examining change in functional microorganisms and metabolic pathways. To enable comparison, the toxicity of positive control with an equivalent Ag+ dose from CH3COOAg was also included. The results indicated that both AgNPs and CH3COOAg enhanced nitrogen fixation and nitrification, corresponding to increased relative abundances of associated functional genes. However, they inhibited denitrification via downregulating nirS, nirK, and nosZ genes as well as reducing nitrate and nitrite reductase activities. In contrast to high dose of AgNPs, low levels increased bacterial diversity. AgNPs and CH3COOAg altered the activities of associated metabolic pathways, resulting in the enrichment of specific taxa that demonstrated tolerance to Ag. At genus level, AgNPs increased the relative abundances of nitrogen-fixing Microvirga and Bacillus by 0.02 %–629.39 % and 14.44 %–30.10 %, respectively, compared with control group (CK). The abundances of denitrifying bacteria, such as Rhodoplanes, Pseudomonas, and Micromonospora, decreased by 19.03 % to 32.55 %, 24.73 % to 50.05 %, and 15.66 % to 76.06 %, respectively, compared to CK. CH3COOAg reduced bacterial network complexity, diminished the symbiosis mode compared to AgNPs. The prediction of genes involved in metabolic pathways related to membrane transporter and cell motility showed sensitive to AgNPs exposure in the soil. Further studies involving metabolomics are necessary to reveal the essential effects of AgNPs and CH3COOAg on biogeochemical cycle of elements in agricultural soil.

Moderate Nitrogen Reduction Increases Nitrogen Use Efficiency and Positively Affects Microbial Communities in Agricultural Soils

Excessive nitrogen fertilizer usage in agricultural often leads to negative ecological and production gains. Alterations in the physical and chemical properties and microbial community structure of agricultural soils are both the cause and consequence of this process. This study explored the perturbation of soil properties and microorganisms in agricultural soils by different nitrogen levels. Soil total nitrogen, total phosphorus, and total potassium decreased in the shallow soil layer with decreasing nitrogen. Changes in nitrogen affected soil organic matter, pH, bulk density, and water content. However, a moderate reduction in nitrogen did not cause significant yield loss; the increased nitrogen use efficiency was the main reason, attributed to the available phosphorus and potassium. Short-term changes in nitrogen had limited effects on soil microbial community structure. Bacteria were more susceptible to perturbation by nitrogen changes. Nitrogen reduction increased the relative abundance of MND1 (1.21%), RB41 (1.96%), and Sphingomonas (0.72%) and decreased Dongia (0.3%), Chaetomium (0.41%), and Penicillium (0.5%). Nitrogen reduction significantly increased the bacteria functional composition of aerobic ammonia oxidation (4.20%) and nitrification (4.10%) and reduced chemoheterotrophy (2.70%) and fermentation (4.08%). Available phosphorus specifically drove bacterial community structure variation in the shallow soil layers of moderate nitrogen reduction treatments. Steroidobacter, RB41, Gemmatimonas, Ellin6067, Haliangium, and Sphingomonas were the main component nodes in this community structure. These results provide insights into the study of nitrogen and microorganisms in agricultural soils.

Does bacterial community succession within the polyethylene mulching film plastisphere drive biodegradation?

Agricultural fields are severely contaminated with polyethylene mulching film (PMF) and this plastic in the natural environment can be colonized by biofilm-forming microorganisms that differ from those in the surrounding environment. In this study, we investigated the succession of the soil microbial communities in the PMF plastisphere using an artificial micro-ecosystem as well as exploring the degradation of PMF by plastisphere communities. The results indicated a significant and gradual decrease in the alpha diversity of the bacterial communities in the plastisphere and surrounding liquid. The community compositions in the plastisphere and surrounding liquid differed significantly from that in agricultural soil. Phyla and genera with the capacity to degrade polyethylene and hydrocarbon were enriched in the plastisphere, and some of these microorganisms were core members of the plastisphere community. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis detected increases in metabolism pathways for PMF plastisphere Xenobiotics Biodegradation and Metabolism, thereby suggesting the possibility of polyethylene degradation in the plastisphere. Observations by scanning electron microscopy (SEM) and confocal laser scanning microscopy demonstrated the formation of biofilms on the incubated PMF. SEM, atomic force microscopy, Fourier transform infrared spectroscopy and water contact angle detected significant changes in the surface microstructure, chemical composition and hydrophobicity change of the films, thereby suggesting that the plastisphere community degraded PMF during incubation. In conclusion, this study provides insights into the changes in agricultural soil microorganisms in the PMF plastisphere and the degradation of PMF.

Antibiotic resistance of microorganisms in agricultural soils in Russia

Antibiotics are medicines that are widely used in livestock production not only for the prevention and treatment of infectious diseases, but also for accelerating the growth of animals. The application of manure for fertilizing agricultural soils leads to the entry into the soil ecosystem not only of the antibiotics themselves, but also the resistance genes to them. In this study, 30 samples of arable soils were tested for the presence of the tet(X) gene, which encodes bacterial resistance to antibiotics of the tetracycline group. Using real-time PCR, it was found that 27 out of 30 soil samples contained tet(X). 52% of these samples were heavily contaminated, 34% had a medium level of contamination and 14% were slightly contaminated by the resistance gene tet(X).

Research and application of method of oxygen isotope of inorganic phosphate in Beijing agricultural soils.

Phosphorus (P) in agricultural ecosystems is an essential and limited element for plants and microorganisms. However, environmental problems caused by P accumulation as well as by P loss have become more and more serious. Oxygen isotopes of phosphate can trace the sources, migration, and transformation of P in agricultural soils. In order to use the isotopes of phosphate oxygen, appropriate extraction and purification methods for inorganic phosphate from soils are necessary. Here, we combined two different methods to analyze the oxygen isotopic composition of inorganic phosphate (δ18OP) from chemical fertilizers and different fractions (Milli-Q water, 0.5molL-1 NaHCO3 (pH=8.5), 0.1molL-1 NaOH and 1molL-1 HCl) of agricultural soils from the Beijing area. The δ18OP results of the water extracts and NaHCO3 extracts in most samples were close to the calculated equilibrium value. These phenomena can be explained by rapid P cycling in soils and the influence of chemical fertilizers. The δ18OP value of the water extracts and NaHCO3 extracts in some soil samples below the equilibrium value may be caused by the hydrolysis of organic P fractions mediated by extracellular enzymes. The δ18OP values of the NaOH extracts were above the calculated equilibrium value reflecting the balance state between microbial uptake of phosphate and the release of intracellular phosphate back to the soil. The HCl extracts with the lowest δ18OP values and highest phosphate concentrations indicated that the HCl fraction was affected by microbial activity. Hence, these δ18Op values likely reflected the oxygen isotopic values of the parent materials. The results suggested that phosphate oxygen isotope analyses could be an effective tool in order to trace phosphate sources, transformation processes, and its utilization by microorganisms in agricultural soils.

Short-term response of nitrifier communities and potential nitrification activity to elevated CO2 and temperature interaction in a Chinese paddy field

While microbial nitrogen transformations in terrestrial ecosystems are known to be affected by global climate change, changes in abundance and composition of mediating microorganisms in agricultural soils under climate change have not yet been well characterized. Here, using well-established molecular fingerprinting techniques and biochemical assays, we tried to analyze changes in nitrifier abundance, composition and activity in the rhizosphere under simultaneously elevated atmospheric CO2 and temperature conditions in a Chinese paddy field. Abundance, rather than community composition of ammonia oxidizing archaea and bacteria (AOA and AOB) responded to the climate change treatments, and the effect was greater on the heading and ripening stages (36–52%) than on the tillering stage (8–26%). Elevated atmospheric CO2 significantly increased AOA and AOB abundance at the heading and ripening stages. Treatment of WA (warming of canopy air) alone did not affect the abundance or community structure of AOA or AOB in the rice rhizosphere at any growth stage. The simultaneous application of CO2 enrichment and warming affected ammonia oxidizer communities differently than independent application of CO2 enrichment or warming, with warming negating the stimulating effect of CO2 enrichment. Phylogenic analysis indicated that all AOA clones fell within the soil and sediment lineage while all AOB clones were classified as Nitrosospira. Although no changes to soil NH4+ or NO3− contents were found, potential nitrification rate generally increased under the treatments with elevated CO2 at all rice growth stages. This could imply a complexity of the joint effect by elevated CO2 on soil properties, plant N uptake and microbial growth. These results suggest that impacts of climate change on N transformation in the rice paddy occur through interactions between effects of climate change on ammonia oxidizer communities and soil properties. Further studies would be required on multiple effects by simulated climate changes on soil properties, N transformations and microbial communities, for a sound understanding of potential changes in N cycling and rice productivity under global climate change.

Biosolids amendment dramatically increases sequestration of crop residue-carbon in agricultural soils in western Illinois

In agricultural soils, a large portion of C in crop residues (i.e., non-harvested plant parts left in the field) is annually lost to atmosphere due to the low C use metabolism of soil microorganisms adapting to the environmental stress (moisture stress and substrate C and N imbalance). In this study, we tested the hypothesis that amending soil with biosolids (treated sewage sludge with high stable organic matter and low C:N ratio) can improve the C metabolism of microorganisms in agricultural soils through alleviation of microbial stress, leading to increased sequestration of crop residue-C in agricultural soils. Biosolids were applied at a mean annual rate of 4.2kgm−2 (dry weight) to eight agricultural fields (biosolids-amended) for 13 years (1972–1984) in western Illinois. Four agricultural fields (unamended) received chemical fertilizer as control. We measured the sequestration rate of crop residue-C in the soils over the span of 34 years (1972–2006) using a 13C technique. We found dramatically greater sequestration rate of crop residue-C in biosolids-amended soil (32.5±1.7% of total crop residue-C) versus unamended soil (11.8±1.6%). Soil microbial metabolic quotient was significantly lower in biosolids-amended than in unamended fields, indicating that biosolid-amendment reduced soil microbial stress and improved microbial C metabolism. The study concludes use of a soil amendment with high stable C and low C:N is a valid approach to transform agricultural soils from current C-neutral status to a C sink. Biosolids represent a good choice of such soil amendments.

Microbial diversity in an Oxisol under no-tillage and conventional tillage in southern Brazil

The no-tillage (NT) system of soil management is recognized as more sustainable than conventional tillage (CT), with an important role played by soil microorganisms. The objective of this study was to estimate differences in soil microbial diversity under NT and CT at different soil depths. For that, bacterial (16S rDNA) and fungal (18S rDNA) communities were evaluated by denaturing gradient gel electrophoresis (DGGE) in a 20-year field experiment established on an Oxisol in southern Brazil on which soybean has been grown in the summer and wheat in the winter. Soil samples were collected at the depths of 0-5, 5-10, 10-20 and 20-30 cm, and submitted to DGGE analyses. The results revealed lower similarity (28%) between bacterial communities in the NT and the CT systems at the 0-5 cm layer. The Shannon index (H) confirmed higher bacterial diversity with NT at all depths, when compared to CT. In relation to fungal communities, higher diversity was detected with CT, especially at the 0–5-cm depth. The results indicate that fungal communities can be more tolerant to environmental stresses related to soil disturbance than bacteria. More emphasis should be given for understanding processes affecting the diversity of microorganisms in agricultural soils, with particular emphasis on tillage systems.

Variable use of plant- and soil-derived carbon by microorganisms in agricultural soils

In this study we used compound specific 13C and 14C isotopic signatures to determine the degree to which recent plant material and older soil organic matter (SOM) served as carbon substrates for microorganisms in soils. We determined the degree to which plant-derived carbon was used as a substrate by comparison of the 13C content of microbial phospholipid fatty acids (PLFA) from soils of two sites that had undergone a vegetation change from C3 to C4 plants in the past 20–30 years. The importance of much older SOM as a substrate was determined by comparison of the radiocarbon content of PLFA from soils of two sites that had different 14C concentrations of SOM. The 13C shift in PLFA from the two sites that had experienced different vegetation history indicated that 40–90% of the PLFA carbon had been fixed since the vegetation change took place. Thus PLFA were more enriched in 13C from the new C4 vegetation than it was observed for bulk SOM indicating recent plant material as preferentially used substrate for soil microorganisms. The largest 13C shift of PLFA was observed in the soil that had high 14C concentrations of bulk SOM. These results reinforce that organic carbon in this soil for the most part cycles rapidly. The degree to which SOM is incorporated into microbial PLFA was determined by the difference in 14C concentration of PLFA derived from two soils one with high 14C concentrations of bulk SOM and one with low. These results showed that 0–40% of SOM carbon is used as substrate for soil microorganisms. Furthermore a different substrate usage was identified for different microorganisms. Gram-negative bacteria were found to prefer recent plant material as microbial carbon source while Gram-positive bacteria use substantial amounts of SOM carbon. This was indicated by 13C as well as 14C signatures of their PLFA. Our results find evidence to support ‘priming’ in that PLFA indicative of Gram-negative bacteria associated with roots contain both plant- and SOM-derived C. Most interestingly, we find PLFA indicative of archeobacteria (methanothrophs) that may indicate the use of other carbon sources than plant material and SOM to a substantial amount suggesting that inert or slow carbon pools are not essential to explain carbon dynamics in soil.