Composition Of Main Microbial Groups Research Articles

The effects of Eisenia fetida and Metaphire guillelmi on the soil micro-food web in a microcosm experiment.

Numerous studies have shown that the function of earthworms may depend on their ecotype and density, which affects how they impact soil microbial and nematode communities. However, it is unclear how different earthworm species and densities alter the composition of soil microbial and nematode communities and how these modifications impact the soil micro-food web. The structural equation model (SEM) is a more accurate tool for identifying the intricate relationships between various trophic levels in the soil micro-food webs than the widely used bivariate data analysis. In order to ascertain the effects of earthworm species, including epigeic earthworm Eisenia fetida and anecic earthworm Metaphire guillelmi, as well as varying densities on the composition of main microbial groups, soil nematodes and their relationships, a microcosm experiment was conducted in a greenhouse. After nine weeks of observation, compared with the control treatments, Eisenia fetida increased the biomasses of total microorganism and bacteria, whereas Metaphire guillelmi decreased the biomasses of total microorganism, bacteria, and gram-positive bacteria, but showed an increase in AMF biomass. Additionally, both two earthworm species decreased the abundance of total soil nematode, bacterivores, and omnivore-predators, which is in contrast with the control treatments. The SEM results indicated that the addition of Eisenia fetida at different densities had indirect negative effects on the abundance of omnivore-predators, as it significantly increased the content of soil organic carbon, ammonium nitrogen, and nitrate nitrogen. The bottom-up effects were found to be the dominant forces, which promoted bacterial-dominated decomposition channels. The addition of Metaphire guillelmi with different density had direct negative impact on bacterivores and fungivores. Moreover, it had indirect negative effects on omnivore-predators by altering the soil properties. The dominant forces were still the bottom-up effects. Our study suggests that different earthworm species have distinct mechanisms that affect the soil micro-food web in different ways.

High additions of nitrogen affect plant species-specific differences in the composition of main microbial groups and the uptake of rhizodeposited carbon in a grassland soil

High additions of nitrogen affect plant species-specific differences in the composition of main microbial groups and the uptake of rhizodeposited carbon in a grassland soil

Co-incorporating leguminous green manure and rice straw drives the synergistic release of carbon and nitrogen, increases hydrolase activities, and changes the composition of main microbial groups

Rice straw (RS) was incorporated into paddy soil together with leguminous green manure (e.g., Chinese milk vetch, Astragalus sinicus L., MV) in a mesocosm-scale experiment and the enzyme activity and composition of main microbial groups were measured. Mixing MV and RS caused a synergistic release of residual C and N, leading to a low C/N ratio at the middle and late decomposition stages of the mixture and shortening the time to complete decomposition. Furthermore, the highest abundances of Gram-negative (G−) bacteria and fungi and the highest activities of α- and β-glucosidase, β-cellobiosidase, β-xylosidase, N-acetyl-glucosaminidase, and acid phosphomonoesterase were observed in the residue mixture, especially at the middle and late stages of the experiment. The residue decomposition rate was positively correlated with residual N and mineral N concentrations. Most hydrolases and both oxidase (phenol oxidase and peroxidase) activities, and G− bacterial (especially 18:1 ω5c, Photobacterium) abundance explained the decomposition of mixing residues. In conclusion, co-incorporation of MV and RS could stimulate their decomposition by retaining a relatively low C/N ratio, enhancing G− bacterial abundance and hydrolase activities. Introducing leguminous green manures in paddy fields may be an effective way to accelerate the decomposition of rice straw.

Divergent mineralization of hydrophilic and hydrophobic organic substrates and their priming effect in soils depending on their preferential utilization by bacteria and fungi

Hydrophilic and hydrophobic organic compounds extracted from 13C-labelled maize residues were incubated with soils to evaluate their mineralization and priming effect (PE) caused by their utilization by microbial groups. Two soils with contrasting soil properties were collected from well-drained upland and water-logged paddy. Mineralization of the 13C-labelled fractions and their PE were quantified by monitoring the CO2 efflux and 13C enrichment during a 40-day incubation. The composition of main microbial groups (bacteria and fungi) involved in the utilization of 13C-labelled fractions was determined based on phospholipid fatty acids (PLFAs) analysis. At the initial stage (6–24 h), hydrophilic fraction had faster mineralization rate (3.6–70 times) and induced 1.5–10 times stronger PE (positive in upland soil and negative in paddy soil) than those of hydrophobic fraction. The 13C-PLFAs data showed that the incorporation of hydrophilic fraction into bacteria was 11.4–16.4 times greater than that into fungi, whereas the hydrophobic fraction incorporated into fungi was 1.0–1.5 times larger than that into bacteria at day 2. This indicated greater contributions of r-strategists (fast-growing bacteria) for the uptake of hydrophilic fraction versus K-strategists (slow-growing fungi) for hydrophobic fraction. Compared with K-strategists, the r-strategists possessed a much faster metabolism and thus triggered stronger apparent PE by accelerating microbial biomass turnover, resulting in higher mineralization and stronger PE for the hydrophilic than hydrophobic fraction. The slower and less mineralization of both fractions in paddy than in upland soils is due to the suppression of microbial activity and substrate utilization under flooding. At the end of 40-day incubation, the cumulative mineralization of hydrophilic and hydrophobic fractions was similar. Consequnently, microbial mechanisms underlying the utilization of organic compounds with contrasting solubility (hydrophilic or hydrophobic) are crucial for evaluating the stabilization and destabilization (e.g., priming) processes of soil organic matter.

Nitrogen deep placement mitigates methane emissions by regulating methanogens and methanotrophs in no-tillage paddy fields

This study investigated the effects of placement of N at different soil depths on CH4 emissions and related microbial communities in no-tillage paddy soil. Five fertilizing treatments, including no N fertilizer, N surface broadcasting, and N deep placement at the soil depths of 5 cm, 10 cm, and 20 cm were applied in the paddy field. The composition of main microbial groups were determined using phospholipid fatty acid (PLFA) analysis. The absolute real-time quantitative PCR was applied to determine the abundance of the methanogenic and methanotrophic populations with mcrA, pmoA, mmoX, and mxaF as the functional gene markers. Compared with N surface broadcasting, the deep placement of N (i) significantly increased the microbial biomass carbon (C) and dissolved organic C by 7–90% and 6–75%, respectively; (ii) significantly enhanced the amount of the total PLFAs by 12–70% and the bacterial PLFAs by 15–82%; (iii) significantly mitigated the CH4 emissions by 6–39%; and (iv) significantly enhanced the abundance of the methanogenic and methanotrophic populations by 16–55% and 13–210%, respectively. The percent changes varied over a wide range due to different N placement depths as well as the seasonal variations. Moreover, structural equation modeling revealed that N deep placement directly or indirectly affected the CH4-related microbial communities through the increased labile soil organic C fractions by activating plant growth and soil microbial abundance, thereby mitigating the CH4 emissions in no-tillage paddy soil.

Nitrogen addition impacts on soil microbial stoichiometry are driven by changes in plant resource stoichiometry not by the composition of main microbial groups in an alpine meadow

Increased nitrogen (N) inputs and subsequent effects on soil microbial stoichiometry have strong influences on organic matter decomposition and nutrient cycling. The effects of N addition on soil microbial stoichiometry are well documented, but we know little about the mechanisms linking between N addition and soil microbial stoichiometry. We examined how the effects of N addition cascade through soil properties (pH, available N (AN), available phosphorus (AP), dissolved organic carbon (DOC), DOC/AN, AN/AP and DOC/AP ratios), plant community composition (grasses, sedges, forbs, and legumes), plant resource stoichiometry (community-level leaf and root C/N/P ratios), and the composition of main microbial groups (phospholipid fatty acids profile) to influence microbial stoichiometry using a 5-year N fertilization field experiment in a Tibetan alpine meadow. We found that N addition changed soil microbial C/N and N/P ratios, but not microbial C/P ratios, indicating plasticity in microbial stoichiometry to increasing N deposition. Moreover, the changes in microbial stoichiometry were driven by N not C and P concentrations. Structural equation modeling revealed that N addition predominantly controlled soil microbial C/N and N/P ratios through plant leaf and root stoichiometry, but not the composition of plant community and main microbial groups. Our findings suggest that N addition-induced changes in plant resource stoichiometry are the core drivers of soil microbial stoichiometry responses to N deposition.

Effects of nitrogen addition on DOM-induced soil priming effects in a subtropical plantation forest and a natural forest

Dissolved organic matter (DOM) plays a key role in soil organic matter (SOM) decomposition via the priming effect (PE). The DOM-induced soil PE is closely related to nutrient availability, especially nitrogen (N). Regardless of the widespread of chronic N addition, how elevated N deposition affects DOM-induced PEs remains poorly understood. To fill this knowledge gap, we studied the effects of N addition, 13C-labeled leaf-DOM (herein DOM) addition, and leaf-DOM plus N addition (DOM+N) on soil PEs in soils of a subtropical Chinese-fir (Cunninghamia lanceolata) plantation and a natural Castanopsis carlesii forest (hereafter referred to as Chinese-fir soil and Castanopsis soil, respectively). Soil properties (e.g., soil organic C, total N, available phosphorus, and ratio of C and N), dissolved organic C (DOC), soil microbial biomass C (MBC), phospholipid fatty acid (PLFA), and enzyme activities were also investigated, because these parameters predominantly affect the intensity and direction of soil priming. The addition of DOM induced positive PEs in the Castanopsis soil but negative PEs in the Chinese-fir soil. In addition, DOM addition increased MBC and fungal abundance and the activities of phenol oxidase (PhOx) and peroxidase (Perox) in the Castanopsis soil but not in the Chinese-fir soil. Compared with DOM-only addition, DOM+N addition significantly enhanced PEs in the Chinese-fir soil but not in the Castanopsis soil. Furthermore, compared with DOM-only addition, DOM+N addition significantly increased MBC, abundance of fungi and AMF, fungi to bacteria ratio (F:B), and activities of four enzymes [β-glucosidase (βG), N-acetyl glucosaminidase (NAG), PhOx, and Perox] in the Chinese-fir soil but not in the Castanopsis soil. The DOM+N addition also had a significant effect on composition of main microbial groups in the Chinese-fir soil but not in the Castanopsis soil. These results suggest the enhanced PE following DOM+N in the Chinese-fir soil was likely mediated by enhanced enzyme production associated with increased fungal abundance. Our study highlights that the effects of increases of DOM on soil C cycling is largely affected by N availability and mediated by the effects on the abundance of soil microbial groups and enzyme activities. Our result also demonstrated a case in which effects of DOM and N addition on soil C cycling differ between a Castanopsis forest and a Chinese-fir plantation forest, with Chinese-fir soil being more sensitive to N addition. This is an important finding that needs to be taken into consideration in estimating the soil C pools.

Short term effects of different green manure amendments on the composition of main microbial groups and microbial activity of a submerged rice cropping system

Green manuring is a feasible agricultural practice to mitigate soil degradation and loss of biodiversity caused by long term application of inorganic fertilizer. However, the effect of the types of green manure (legume vs non-legume) on soil microbial groups and activities are largely not known. Field experiments were conducted to investigate the effects of incorporating two green manures that originated from residues of barley (Hordeum vulgare) and hairy vetch (Vicia villosa), on microbial groups, biomass, enzyme activities, nutrient availability of soil, and crop yield in a mono-rice cropping system. Green manure biomasses were applied on an equal nitrogen biomass basis. We found that, compared to inorganic fertilizer, green manures amendment significantly increased composition of main microbial groups, microbial biomass C (MBC) and hydrolase activities of soil. Total PLFAs, Gm + bacteria, fungi and actinomycetes PLFAs were markedly increased by the barley residue amendment, whereas Gm- bacteria PLFA was mostly increased by the hairy vetch residue amendment. The higher hydrolase activities involved in C cycling were observed in the barley treatments, whereas soil enzyme activities involved in N and P cycling were higher in the hairy vetch treatments. Probably, differences between the two treatments dependent on different chemical composition of the green manures incorporated into the soil and their mineralization controlled by the soil C:N ratio. A decrease in oxidative enzyme activities and higher fungi: bacteria ratio as a result of the green manure amendment, in particular barley, suggested the potential of barley biomass incorporation to enhance C storage in submerged rice cropping systems.

Effect of long-term fertilization on decomposition of crop residues and their incorporation into microbial communities of 6-year stored soils

To investigate the effects of long-term fertilization on microbial decomposition of residues and priming effect (PE), 13C-labeled maize (Zea mays L.) residues were supplied to arable soils with a 20-year application of compost (COM), mineral NPK fertilizer (NPK), or without any treatments, the no-fertilizer control (NF). The soils that had been stored for 6 years were used in the present incubation experiment. The release of CO2–C and the microbial incorporation of residue-derived C determined by phospholipid fatty acids (PLFAs) analysis were monitored over a 90-day incubation period. Residue additions significantly increased cumulative CO2–C emission and induced positive PE. Cumulative residue-derived CO2-C emission and PE mainly occurred within the first 15 days. The COM soil had significantly higher cumulative residue-derived CO2–C emission but lower PE than the NF and NPK soils. Residue additions significantly increased microbial abundance and changed the composition of main microbial groups. The COM soil showed a significantly lower relative fungal abundance (mol%) but a higher relative actinomycetes abundance than the NF and NPK soils. The incorporation of residue-derived C within fungi was the highest among all the main microbial groups and decreased from 15 to 45 days, while the incorporation of residue-derived C within actinomycetes increased with time in three soils. The incorporation of residue-derived C within fungi was the highest in the COM soil over the course of incubation. The long-term compost input promoted fungal use of residue C and stimulated residue decomposition.

Relationship between the chemical structure of straw and composition of main microbial groups during the decomposition of wheat and maize straws as affected by soil texture

Field decomposition of wheat and maize straws was monitored for 20 months using litterbag method in Calcaric Fluvisol soils with three different textures (sand, sandy loam, and silty clay). Residual straw samples were collected at 0 or after 4, 6, 10, and 20 months of decomposition. The chemical structure of straw was analyzed by solid-state 13C nuclear magnetic resonance (13C-NMR) spectroscopy, and the composition of main microbial groups was evaluated by phospholipid fatty acid analysis. Regardless of the straw type and soil texture, the straw biomass and C loss increased steadily in the first 10 months and then leveled off in the following 10 months; both the chemical structure of straw and the composition of main microbial groups differed during incubation. During the first 4 months of wheat straw degradation, the decrease in di-O-alkyl and O-alkyl C and the increase in alkyl and N-alkyl/methoxyl C contents were related to the enrichment of fungi (18:1ω9c) and Gram-negative bacteria (18:1ω7c and 16:1ω7c), while the degradation of maize straw was associated with the decrease in the fungal (18:1ω9c) abundance and the increase in the abundance of Gram-negative (18:1ω7c and 16:1ω7c) and Gram-positive (a15:0) bacteria. During the 6–10-month period, the decrease in di-O-alkyl and O-alkyl C and the increase in alkyl, aryl, and carboxyl/amide C contents were related to the enrichment of arbuscular mycorrhizal fungi (AMF) (16:1ω5c) and Gram-negative (cy19:0ω8c) bacteria and the decrease in fungal (18:2ω6,9c) abundance, with AMF playing an important role in the degradation of both straw types. The altered chemical structure of wheat and maize straws had opposite links with fungal abundance during the first 4 months, while alterations occurring during the 6–10-month period mainly depended on the variation in the AMF abundance.

Effects of converting a temperate short-rotation coppice to a silvo-arable alley cropping agroforestry system on soil quality indicators

Short-rotation coppices (SRC) and alley cropping agroforestry systems (ACS) provide ecosystem services and environmental benefits. Particularly, their role in improving soil quality has frequently been emphasised. However, the economic lifetime of fast growing tree plantations may be limited, making a transition indispensable. Since information on effects of such land-use changes on soil microbial properties is scarce, the aim of this study was to assess effects of converting a German poplar-based SRC to a silvo-arable ACS, comprising rootstock incorporation and reduced tillage, on soil quality indicators after one year. Soils were sampled under poplars and within the re-converted alleyway. Distance transects were considered to further include potential beneficial effects of remaining trees on alleyway topsoil quality. We analysed soil organic carbon (SOC), total nitrogen, soil microbial biomass C and N, ergosterol, microbial activity (enzyme activities, multi-substrate-induced respiration rates), ratios relative to SOC, fungal abundance and microbial functional diversity at two topsoil depths (0–5, 5–20 cm). Repeated measures mixed effects models were calculated for each depth, considering spatial dependence structures and potential heterogeneity of abiotic factors (pH, clay contents). SRC to ACS conversion decreased SOC, microbial biomass and activity in upper topsoils within the arable alleyway, irrespective of tree distance. Furthermore, shifts in the composition of main microbial groups towards a lower fungal abundance and functional diversity were observed. Reductions of fungal indices were also identified in lower topsoils. Unexpectedly, results demonstrated that partial conversion of a SRC back to arable cropping decreased soil quality within as little as one year.

Organic carbon quality, composition of main microbial groups, enzyme activities, and temperature sensitivity of soil respiration of an acid paddy soil treated with biochar

The role of soil organic C (SOC) quality affecting microbial community composition and function under biochar application is poorly understood. We investigated the relationship between the pool size and chemical composition of SOC; composition of main microbial groups; enzyme activities involved in C, N, and P cycling; and soil respiration in a rice paddy amended with biochar for 20 months in a laboratory experiment at 15, 25, and 35 °C. Soil labile and recalcitrant organic C pools were determined by a two-step sulfuric acid (H2SO4) hydrolysis method. The chemical composition of SOC was determined with 13C-nuclear magnetic resonance spectroscopy. The biochar amendment at 20 and 40 t ha−1 significantly decreased the soil labile C pool I (extracted by 5 N H2SO4), alkyl, and carbonyl C contents and increased the recalcitrant C pool (acid-resistant) and aromatic C contents and the aromatic C to O-alkyl C ratio. The phospholipid-fatty acid concentrations and soil enzyme activities were unchanged by biochar application at 10 and 20 t ha−1, but both were increased at 40 t ha−1. Biochar increased the ratio of gram-positive (G+) to gram-negative (G−) bacteria and decreased that of fungi to bacteria. The recalcitrant C pool and aromatic C contents were positively correlated to the G+ bacteria abundance and were important factors in shaping composition of the main microbial groups and improving enzyme activities. Biochar application at 40 t ha−1 lowered soil respiration rates at 15 and 25 °C by decreasing labile C pool and increasing C recalcitrancy while increased temperature sensitivities of soil respiration at 25/15 °C and 35/25 °C by stimulating microbial abundance and enzyme activities. Together, our results suggest that biochar soil amendment shifted microbial community composition and function through influencing the composition of SOC.

Similar spatial patterns of soil quality indicators in three poplar-based silvo-arable alley cropping systems in Germany

Alley cropping systems (ACS) are regarded as a sustainable land-use alternative that provides ecosystem services, assuming that beneficial tree effects extend towards crop alleys. However, the spatial range of these effects has rarely been considered. The objective of this study was to investigate soil quality indicators at different distances from trees in three German silvo-arable ACS. We analysed soil microbial biomass C and N, ergosterol, microbial activity (enzyme activities, substrate-induced respiration rates) and their functional diversity (MicroResp™ method) in topsoils. Furthermore, fungal abundance and fungal and bacterial contribution to microbial residues (amino sugars) were determined. Tree effects on soil quality indicators were estimated for each depth, for the first time considering both, spatial dependence and abiotic factors (pH, clay content) using mixed effects models with repeated measures. Additionally, differences between soil depths were tested. Analysis combining the three ACS revealed a generalisation of effect sizes and spatial range of tree effects on soil quality indicators. Tree implementation in arable systems increased SOC, microbial biomass and activity in upper topsoils and shifted the composition of main microbial groups towards a higher fungal abundance and functional diversity. Soil quality indices decreased with increasing depth. However, in alleys, no differences between distances from trees were observed. Results demonstrate that ACS are capable to enhance soil quality mediated by microorganisms under trees within 5–8 years. Long-term studies are required to estimate whether beneficial tree effects extend towards crop alleys and deeper soil layers when systems are mature.

Effects of O3 stress on physico-chemical and biochemical properties and composition of main microbial groups of a soil cropped to soybean

Tropospheric O3 (ozone) stress can negatively affect forest productivity and crop yields. Yet, relatively little attention has been paid to the effects of O3 stress on belowground system. Here, a pot experiment was conducted in open top chambers to monitor the response of physico-chemical properties, main microbial groups, and potential enzyme activities of a soil cropped to soybean (Glycine max; a highly sensitive species to O3) and exposed to background O3 concentration (45 ± 5 ppb, control) and O3 stress (80 ± 10 ppb, O3+ and 110 ± 10 ppb, O3++) with sampling at branching, flowering, and podding stages. The growth of soybean was significantly inhibited by O3 stress, which showed significant effects on soil microbial biomass C and pH during the whole growth of soybean at the highest concentration. The O3++ stress significantly decreased soil pH at flowering stage, and increased soil pH at podding stage; the O3+ stress and growth stage × O3+ stress showed significant influences on the potential activities of acid phosphomonoesterase, invertase, and amylase. The O3 stress significantly reduced the abundances of total PLFAs (phospholipid fatty acid), bacterial PLFAs, and AMF (arbuscular mycorrhizal) PLFAs at branching and podding stages. Our results suggest that the main soil microbial groups might be indirectly affected by the O3 stress through the alteration of soil physico-chemical properties with changes in the potential enzyme activities of soil.