Total Microbial Biomass Research Articles

Agricultural practices influence biological soil quality indicators in an irrigated semiarid agro-ecosystem

A study was conducted to investigate how soil biological measurements can be used to indicate differences in soil quality in arid and semiarid agroecosystems. The objectives were to assess soil biological quality indicators under different land management practices and at different depths and to explore the relationships between soil microbial community and organic matter fractions. Soil samples were collected from three replicates of six land management systems at 0–5 cm and 5–15 cm soil depths. Four management systems had medium to fine soil texture including a permanent grass field with tall fescue (Lolium arundinaceum [Schreb]; TFC), peach orchard with clover understory (Prunus persica with Trifolium repens L.; PCC), alfalfa field (Medicago sativa; ALF) and conventionally tilled soil with an annual crop rotation (CTC). Two management systems, including a young cottonwood tree orchard (Populus fremontii and Populus deltoides; CWS) and conventionally tilled soil in annual crop rotation (CTS), had coarse soil texture. Management systems had significant impacts on most of the soil biological indicators assessed at the two depths with both depths responding similarly to management practices. For the soil biological indicators that showed differences, the TFC generally had the most favorable indicator measurements compared to other management systems. The principal component analysis showed a clear separation between the management systems and microbial communities at both soil depths. The ordination pattern was structured by soil textural differences between medium to fine-textured soils from TFC, PCC, ALF, and CTC fields and coarse-textured soils (CWS, CTS). Spearman’s correlation coefficients (rs) showed that the soil organic matter (rs = 0.85, P = 0.001) and the permanganate oxidizable carbon (rs = 0.93, P = 0.001) were significantly correlated with the total microbial biomass at 0–5 cm soil depth. Also, the soil organic matter (rs = 0.84, P = 0.001) was significantly correlated with the total microbial biomass at 5–15 cm soil depth. This study suggests that in semiarid agroecosystems, management practices with permanent covers have the potential to improve soil quality, and soil texture may also influence the directional changes in soil quality within this region.

The soil microbiome unveils strong imprints of artificial erosion after 27 years

Soil erosion is a severe and widespread form of land degradation worldwide, and is being exacerbated by effects of climate change, such as increased storm frequency and intensity. It is important to study the impact of soil erosion on the soil microbiome because soil microbes are crucial drivers of many important soil biological processes in agriculture. In 2016 and 2017, we sampled a simulated soil erosion field trial established in 1990 to investigate the effects of different depths of topsoil removal and restorative soil amendments on soil pH, microbial biomass carbon (MBC) and the activities of enzymes that mediate C, nitrogen (N), phosphorus (P), and sulfur (S) cycling, plus the diversity and composition of soil prokaryotic (bacteria and archaea) and fungal communities. The one-time (1990) treatments consisted of a split-plot combination of three depths of topsoil removal (0, 10, and 20 cm) as main plots, and three restorative soil amendments (check, topsoil, and cattle manure) as subplots. Soil pH was higher in the eroded treatments than the noneroded treatment, but the opposite was observed for MBC and the activities of β-glucosidase (C cycling) and N-acetyl-β-glucosinidase (C and N cycling). The restorative amendments did not affect soil pH, MBC, or enzyme activities. The relative abundances of the archaea Thaumarchaeota was higher in noneroded treatments than in eroded treatments, but the reverse was observed for the bacteria Chloroflexi, Gemmatimonadetes, Planctomycetes, and Verrucomicrobia. For fungi, the relative abundance of Basidiomycota was lower in eroded treatments than in the noneroded treatment, but the opposite was true for Mortierellomycota. The β-diversity analyses also showed different prokaryotic and fungal community structures between eroded and noneroded treatments, but the restorative amendment effects were less distinct. Therefore, soil erosion and excavation can have lasting imprints on the soil microbiome, particularly negative imprints on total microbial biomass and its C and N cycling potential, while imprints of restorative measures such as manure or topsoil amendment were not as strong. A single desurfacing event has effects that last for decades, and our efforts to reverse them are largely ineffective when applied only once.

Vascular plant and cryptogam abundance as well as soil chemical properties shape microbial communities in the successional gradient of glacier foreland soils

In the glacier forelands, microbes play a fundamental role in soil development and shaping the vegetation structure. Such ecosystems represent various stages of soil development and are, therefore, an excellent place to study the interrelationship between soil, plants, and microorganisms. The aim of the study was to assess the effects of vegetation and soil physicochemical properties developing after glacier retreat on soil microbial communities. Specifically, abundance, species richness and the composition of arbuscular mycorrhizal fungi (AMF), as well as microbial biomass and community structure in soils were compared between plots established in 800-meter transects of three glacier forelands in northern Sweden. The cover of vascular plants and cryptogams, soil C content, AMF spore density and species richness, AMF biomass indicators, total microbial biomass, and bacterial phospholipid fatty acids (PLFA) were significantly and positively related to the distance from the glacier terminus. On the other hand, macronutrient concentrations and pH decreased along with increasing distance. No significant impact of the distance from the glacier terminus on the ratio fungal/bacterial PLFA was observed. Moreover, we found a significant effect of both glacier and the distance from the glacier terminus on the microbial community structure. AMF species richness and spore density in the glacier forelands were generally low, which is probably due to a limited supply of inoculum in primary successional ecosystems. Most microbial biochemical markers and AMF parameters were positively associated with the number of arbuscular mycorrhizal plant species and vascular plant and lichen cover as well as C content in soil, whereas negatively with soil macronutrients and pH. This could be related to an increase in plant cover and a decrease in soil nutrient levels as plant succession progresses. Our results showed that vegetation, soil C content, and microbial communities are interlinked and exhibit concordant patterns along successional gradients.

Relationships between soil properties, vegetation and soil biota in extremely sulfurized mine soils

The study aimed to assess the influence of high sulfur (S) contamination and the properties of the reclaimed (e.g. neutralization/liming of contamination) soil on the regeneration of soil vegetation and fauna in the example of the former sulfur mine. An attempt was also made to assess minimal conditions for the development of soil microorganisms and mesofauna depending on the type of cover (reforestation/herbaceous vegetation/bare soil). Thirty sample plots were situated on three mainland categories–– i) plant cover vegetated mainly Pinus sylvestris L. (Scots pine stand category), ii) Betula pendula Roth (silver birch stand category), and iii) degraded area with bare soil (Bare_Central – in the central place of the plot and Bare_Edge usually 5.5 m from Bare_Central, Veg – 1 m from Bare_Edge). Basic soil chemicals (as pH, electrical conductivity EC, total sulfur S, total nitrogen TN, total organic carbon TOC), biological parameters (e.g. fungal and bacterial phospholipid fatty acids PLFAs, GRAM+, GRAM−, actinobacteria, total microbial biomass TM), and mesofauna density were analyzed to assess the level of contamination and colonization of the area by plants and soil fauna. The PLFA and the presence of soil microorganisms, always increased from a central point (Bare_Central) to an outer one (Bare_Edge) that was very close (about 1 m) to the vegetation (Veg). However, the highest biological parameters was found in Veg near the bare soil than in the stands with Scots pine. It was found that the highest microbiological biomass was positively correlated with the occurrence of vegetation. Mesofauna was limited by a high content of sulfur in the soil and high EC. Silver birch stands, through the larger and more favorable properties of plant litter, create conditions in which the growth of microorganisms is much greater than under Scots pine stands. On the other hand grasses area with single Scots pine was characterized by higher biological parameters than with the silver birch. In the plots with tree stands it was quite the opposite. To properly restoration this type of place, it is necessary to ensure the accuracy of the technical measures performed. The best effects of activating soil microorganisms are the introduction of trees with appropriate density. The activity of soil microorganisms allows for the growth of herbaceous vegetation, which will be a start-up source of organic matter and nourishment for soil biota. Herbaceous vegetation will create a good mixture with hard decomposed pines litterfall.

Integrated Application of Trichoderma Mixture and NPK Enhances the rice Productivity in Sodic Soil

Abiotic stresses due to changing environmental conditions and intensive agriculture are causing soil salinity and sodicity leading tosoil deterioration. It directly affects nutrient availability and uptake and reduces plant productivity. The microorganisms are known toimprove the availability of nutrients in the soil and therefore, the present work aimed to maximize the use of applied fertilizers and boostthe productivity. The effects of the Trichoderma mixture (TrichoMix) and NPK on plant growth and rice yield in degraded land underfield conditions was studied. The abiotic stress tolerant Trichoderma strains comprising of T. koningiopsis (NBRI-PR5) and T. asperellum(NBRI-K14) were used in the treatments (i) Control (Cont.), (ii) NPK, as per recommended dose (NPK100%) (iii) Trichoderma mixture (NBRIPR5+NBRI-K14) (TrichoMix) (iv) TrichoMix + NPK50%. Significantly higher plant growth and yield (6.57q/h) was obtained in TrichoMix+NPK50% treatment. The improvement in rice production in the treatment TrichoMix +NPK50% was ascribed to the significant changes insoil physiochemical characteristics such as water holding capacity (35%), bulk density (40%), total organic carbon (42%), available N(39%), P (44%), K (48%) and microbial biomass carbon (88%). The results conclude that the mixture of T. koningiopsis (NBRI-PR5) and T.asperellum (NBRI-K14) may be recommended as sodic soil amendment to increase plant growth and yield in combination with chemicalfertilizers to support rice cultivation.

Single-cell view of deep-sea microbial activity and intracommunity heterogeneity.

Microbial activity in the deep sea is cumulatively important for global elemental cycling yet is difficult to quantify and characterize due to low cell density and slow growth. Here, we investigated microbial activity off the California coast, 50-4000 m water depth, using sensitive single-cell measurements of stable-isotope uptake and nucleic acid sequencing. We observed the highest yet reported proportion of active cells in the bathypelagic (up to 78%) and calculated that deep-sea cells (200-4000 m) are responsible for up to 34% of total microbial biomass synthesis in the water column. More cells assimilated nitrogen derived from amino acids than ammonium, and at higher rates. Nitrogen was assimilated preferentially to carbon from amino acids in surface waters, while the reverse was true at depth. We introduce and apply the Gini coefficient, an established equality metric in economics, to quantify intracommunity heterogeneity in microbial anabolic activity. We found that heterogeneity increased with water depth, suggesting a minority of cells contribute disproportionately to total activity in the deep sea. This observation was supported by higher RNA/DNA ratios for low abundance taxa at depth. Intracommunity activity heterogeneity is a fundamental and rarely measured ecosystem parameter and may have implications for community function and resilience.

Evaluation of sedimentary bacterial community dynamics and contamination assessment of lower Des Plaines River

Urban rivers often contain elevated concentrations of contaminants such as organic pollutants and heavy metals which can be amplified in lotic ecosystems receiving effluents from wastewater treatment plants (WWTP). However, the impact of WWTPs on the microbial parameters of the urban river sediments has not been well documented compared to urban surface water. Collecting sediment samples at five different locations over a 9,000 m transect during four sampling periods, we investigated spatiotemporal variations of microbial parameters in sediments of lower Des Plaines River; the largest effluent-dominated stream in the United States and the effects of sediment physicochemical properties on the variations were explored. We reported reduced microbial biomass, CFUs, and distinct bacterial communities at the WWTP outfall compared to other sites, indicating that WWTP effluents have the potential to moderate bacterial community structure. Seasonal variations in the sedimentary bacterial community structure were evident regardless of the spatial variations imposed by the effluents. Our community-level physiological profiling of the sedimentary bacterial community structure indicated that temperature was more important than water chemistry, whereas total microbial biomass by phospholipid phosphate analysis responded to the influences of both temperature and water chemistry. Metal concentrations showed values that fall within the “fair” to “very poor” range of biological conditions outlined by the Midwest Biodiversity Institute. We posit that the increased sediment metal loads select for metal-tolerant microorganisms that help to maintain microbial biomass. In the spring, sequencing of bacterial 16S rRNA genes revealed significant effects of effluent on bacterial community composition at the WWTP outfall, showing increases in abundances of Caldilinea, Candidatus, Allochromatium, Sulfuritalea, and Nitrospira sequences, linked to anthropogenic inputs from WWTP effluents. Given that human dependence on effluent-dominated ecosystems for water resources will increase with rapidly increasing urbanization, studies focusing on remediation and policy changes are dire to develop effective management of existing urban rivers.

Microbial utilization of photosynthesized carbon depends on land-use

The release of organic compounds from plant roots (rhizodeposits) and their subsequent utilization by soil microbial communities is a key process linking atmospheric and terrestrial carbon (C) and nutrient cycling. However, the effects of land-use types on rhizodeposit-mediated alteration of microbial community structure and its consequences for soil C cycle are still, largely, unknown. Therefore, we used 13C-PLFA-SIP to evaluate the rhizosphere C fluxes to microorganisms in a monoculture crop (oilseed rape, Brassica napus L.), a mixed grassland (dominated by Lolium perenne L. mixed with clover Trifolium repens L.), and a tree (willow, Salix schwerinii E.L. Wolf and Salix viminalis L.) within an agroforestry system. Though harboring similar total microbial biomass, less 13C was recovered in microorganisms in soil under willow (0.017 % of 13C input) after 14 days as compared to rape (0.03 %) and grassland (0.09 %). Across three land use types, gram negative bacteria incorporated most of the 13C (28–42 % of total 13C labeled PLFAs), followed by fungi and gram positive bacteria (12–18 %) and less abundance groups (e.g. actinomycetes, <5 %). The arbuscular mycorrhizal fungal biomarker 16:1ω5c was enriched with 13C in soil under grassland (8 % of total 13C labeled PLFAs). The 13C incorporation into gram positive bacteria was higher in soil under willow than under grassland and rape. By contrast, 42 % of total 13C labeled PLFAs were attributed to gram negative bacteria in soil under rape. Overall, our results demonstrated that pronounced differences in microbial community structure and subsequent microbial C utilization between land-use types could affect soil C cycles and storage.

Long-term organic fertilizer additions elevate soil extracellular enzyme activities and tobacco quality in a tobacco-maize rotation.

Organic fertilizer is effective in improving soil quality, and promoting crop growth. Combined organic and inorganic fertilization has been proved as a more favorable way to tobacco yield and quality. However, the mechanisms underlying tobacco yield and quality under combinations of different organic and inorganic fertilizer remain unclear. We conducted a 12-year tobacco (Nicotiana tabacum L.)-maize crop rotation field experiment in Yanhe experimental station, China to examine the yields and qualities of tobacco, soil nutrients, and extracellular enzyme activities associated with carbon, nitrogen, and phosphorus cycles in response to different fertilization treatments. Five fertilization treatments (no fertilization; 75 kg N fertilizer ha–1; 450 kg oil cake ha–1 + 75 kg N fertilizer ha–1; 15,000 kg pig dung ha–1 + 60 kg N fertilizer ha–1; 3,000 kg straw ha–1 + 75 kg N fertilizer ha–1) were applied to tobacco while maize was fertilized with inorganic compound fertilizers. After 12 years of tobacco-maize rotation, the results showed that organic fertilizer additions elevate tobacco yield and quality, and the soil extracellular enzymes activities. Gram-negative bacteria, actinomycetes, and total soil microbial biomass were increased by organic fertilizer additions, both plant-based (oil cake and straw) and animal-based (pig dung) organics. The levels of soil organic matter, total organic carbon, total phosphorus and available phosphorus are higher in pig dung addition treatment than oil cake and straw additions. By variance analysis with respect to fertilization treatments, organic sources differentially affected the activities of diverse soil enzymes. The redundancy analysis gave that yield and quality of tobacco leaves (upper, middle, and lower leaves) positively related to soil extracellular enzyme activities. Based on analysis of yield and quality of tobacco leaves with extracellular enzyme activities and soil nutrients, it is suggested animal-based organic fertilizer, thus pig dung, should be used in combining with chemical fertilizers to improve the quality of tobacco and soil nutrients.

Global patterns and controls of the soil microbial biomass response to elevated CO2

Elevated CO2 concentrations (eCO2) have been widely observed to stimulate microbial growth. However, the effect of eCO2 on soil microbial biomass may depend on several factors and their interactions, such as the increase in atmospheric CO2 levels, experimental duration and mean annual precipitation (MAP). We conducted a global meta-analysis from 62 studies that included the responses of soil microbial biomass to eCO2. We found a significant positive eCO2 effect on the bacterial biomass (+9.1 %), fungi (+11 %), arbuscular mycorrhizal fungi (AMF) (+10.2 %) and actinomycetes (ACT) (+16.4 %). The positive effects were mainly observed in studies with low eCO2 levels (≤200 ppm) rather than high levels of eCO2 (>200 ppm), which could be attributable to soil N limitation. It was also found that eCO2 had a significant positive effect on soil microbial biomass in the short term (≤3 y) and under a high MAP (>800 mm). Importantly, we revealed interactive effects between the eCO2 levels, experimental duration on soil microbial biomass. With an increase in eCO2, the total microbial biomass (TMB), bacterial biomass and fungal biomass decreased over the long term (>3 y). These findings indicate the need to incorporate interactions between eCO2 and environmental factors into ecosystem models, to predict future global climate change effects more accurately and their impact on ecosystem functions.

Long-Term Wheat-Soybean Rotation and the Effect of Straw Retention on the Soil Nutrition Content and Bacterial Community

Straw retention and wheat-soybean rotation play critical role in maintaining soil quality. However, the correlation between bacterial diversity and community structure, and soil nutrients is unknown, and a systematic understanding of their responses to straw retention is lacking. In the field experiment, the straw retention treatments included no straw (NS), half straw (HS), and total straw (TS) retention during long-term wheat-soybean rotation. The mean contents of soil total nitrogen (TN), nitrate-N (NO3−-N), and microbial biomass nitrogen (MBN) increased by 15.06%, 21.10%, and 38.23%, respectively, with straw retention relative to NS, while that of ammonium-N (NH4+-N) reduced by 3.68%. The concentration of carbon components increased as straw retention increased. The levels of soil dissolved organic carbon (DOC), microbial biomass carbon (MBC), and soil organic carbon (SOC) increased by 4.34%, 7.63%, and 9.34%, respectively, with straw retention relative to NS. Soil bacterial alpha diversity was reduced with straw retention. Soil pH and nutrient content were identified as the main factors affecting the soil microbial diversity and structure at the phylum level. Accordingly, straw retention and soybean-wheat rotation enable sustainable agriculture in the dryland of northern China.

Influence of land‐use changes on microbial community structure and diversity in a semiarid region

AbstractLand‐use change and the conversion of land into croplands is one of the main drivers of soil degradation and the loss of soil organic carbon. Few studies have evaluated the impact of the expansion of the agricultural frontier on soil microbial communities in the Gran Chaco region in South America; therefore, the objective of this study was to explore how soil microbial communities respond to land‐use changes in a semiarid region of Argentina. The land uses selected were total and selective clearing with livestock (TC‐livestock and SC‐livestock), total clearing with agriculture (TC‐agriculture), and an undisturbed site (R‐Chancaní). Our results suggest that microbial abundances were strongly influenced by seasonal changes. In both seasons, the lowest values of total microbial biomass were observed in TC‐agriculture and TC‐livestock. In the wet season, TC‐agriculture had the lowest fungal abundance, and both total clearing sites (TC‐livestock and TC‐agriculture) had higher bacterial abundance than the other sites. Our data also showed that the Shannon and richness indices were highest at the farming sites, indicating a similar tendency in the diversity indexes in both dry and wet seasons. According to Pearson correlation analysis, humic substance (HS) content was a key driver influencing soil microbial communities, demonstrating that high HS content may significantly increase bacteria, fungi, and total phospholipid fatty acids. Microbial composition highly depended on seasonal changes. Overall, our results suggest that land‐use change altered microbial community structure and bacterial diversity, and that HS content played a crucial role in driving changes in soil microbial composition.

Comparison of Surface Water or Treated Municipal Wastewater Irrigation on Alfalfa Establishment, Soil Fertility, and Soil Microbial Conditions

Water scarcity for agricultural irrigation is increasing globally while generation of treated municipal wastewater (TWW) is increasing due to urban expansion. Municipalities seek uses for their TWW, which is safe to apply to forage crops. Alfalfa (Medicago sativa) is the most important forage crop worldwide being adapted to a wide range of environmental factors, including irrigation with low quality water. A strip plot study with four replications at New Mexico State University’s Rex E. Kirksey Agricultural Science Center at Tucumcari, NM USA, compared the effects of surface water (SW) and TWW on alfalfa establishment and soil fertility and microbial growth. Alfalfa established equally well when irrigated with equal amounts of TWW or SW. After one year, the application of TWW increased soil P and plant N and P more so than SW. Most microbial soil health indicators were positively increased by alfalfa establishment in virgin soil; however, the effect was greater with TWW compared with SW (1147, 1184, 1961, and 4991 nmol g−1 for total microbial biomass of soil irrigated with SW and TWW at seeding and after one year, respectively, LSD0.05 = 710). Thus, TWW irrigation could reduce applied fertilizer P to meet alfalfa’s requirement and increase soil health compared with SW.

Potential effects of soil chemical and biological properties on wood volume in Eucalyptus urophylla × Eucalyptus grandis hybrid plantations and their responses to different intensity applications of inorganic fertilizer.

Long-term and high-intensity application of inorganic fertilizer leads to a strong variation of soil characteristics. The changes in soil chemical and biological properties can significantly affect the yield of Eucalyptus plantation. However, the mechanism of soil chemical properties affecting wood volume mediated by biological factors is not clear. The purpose of this study was to identify which soil properties were affected by different fertilization intensities and to disentangle the dominant factors affecting Eucalyptus volume. After clear felling evergreen broad-leaved forest, a Eucalyptus plantation was established that was coppiced every 5 years and fertilized every year. Within this plantation, areas with different treatments were established. These treatments were a 5-year growth period (low); two times 5-year growth period (medium); and three times 5-year growth period (high). In each treatment area and in a nearby evergreen broad-leaved forest (EBLF Control), five sample plots per treatment were set up. Various biological and chemistry analyses (18 in total) were related to determining the most important path and index for optimizing Eucalyptus plantation. The analysis of variance of enzyme activity and microbial biomass showed that the soil biological characteristics decreased over 10 years of plantation, and the enzyme activity was close to the state of EBLF control in medium, while the microbial biomass failed to return to its original state during continuous planting. Redundancy analysis results show that there was a strong correlation in chemical indicators and biological characteristics. Partial least square structural equation model showed that total phosphorus, nitrate nitrogen, urease, catalase, and microbial biomass nitrogen and phosphorus were the most influential soil biochemical factors, and the indirect effect of chemical properties on volume was achieved by microorganisms through enzyme activity. Continuous planting and large-scale application of inorganic fertilizer would lead to a decrease in plantation yield and fertilizer utilization efficiency and would affect the microbial biomass and enzyme activity by destroying the stability of soil chemical properties.

Effects of Phytoremediation on Microbial Biomass, Composition, and Function in a Sulphide-Rich Tailing From a Metal-Contaminated Region

Mining activities lead to serious land deterioration and large scale mine waste generation. Reclamation has been carried out on several technogenic materials to encourage the development of soils. To date no detailed studies have been conducted to assess if soil developed in reclaimed tailings can be suitable for microbial community sustainability and associated plant population. This study investigated if 1) soil metal contamination affects microbial biomass and composition in sulphide tailings and 2) phytoremediation of tailing increases microbial abundance, diversity, and function. Microbial biomass was assessed using Phospholipid fatty acid analysis (PLFA). Soil bacterial and fungal microbiota was determined by high throughput sequencing of 16S rRNA gene for bacteria and internal transcribed spacer region for fungi using the Illumina platform. Total copper, nickel, iron, and titium were higher in unreclaimed sites compared to vegetated areas but the total microbial biomass was significantly higher in reclaimed sites compared to reference areas. More importantly, the levels of microbial biomass were not impacted by metals since the bioavailable Cu, Ni, and Ti were low in all the sites. Site-specific bacterial and fungal genera were identified. Proteobacteria was the most dominant bacterial phylum while Ascomicota was the predominant fungal phylum. Interestinlgy, Acidiferrobacter, an acidophilic, thermotolerant and facultatively anaerobic was the most predominant genus in unreclaimed site that is characterized by extreme acidity (pH = 2.8). Analysis of microbial diversity revealed higher Chao 1, # of OTUs, Shannon index, and species richness in bacterial and fungal populations from reclaimed sites compared to controls. The levels of β-glucosidase (BG), cellobiohydrolase (CBH), β-N-acetylglucosaminidase (NAGase), aryl sulfatase (AS), acid phosphatase (AP), alkaline phosphatase (AlP), glycine aminopeptidase (GAP), and leucine aminopeptidase (LAP) activities were significantly higher in vegetated sites compared to reference areas. Strong positive correlation coefficients were observed between soil organic matter and total microbial biomass (r = 0.99). These two factors were positively correlated with enzymatic activities and bacterial population diversity. Overall, newly developed soils can sustain diverse microbial communities and associated vegetations.

Spatial and Temporal Changes of Soil Microbial Communities in Field Tomato Production as Affected by Anaerobic Soil Disinfestation

Anaerobic soil disinfestation (ASD) has been demonstrated as an effective alternative to pre-plant chemical soil fumigation (CSF) commonly used to control soilborne pathogens. However, the ASD effects on spatial and temporal changes in soil microbial communities remain poorly understood in production systems with low soilborne disease pressure. The objective of this study was to assess the influence of ASD treatments on soil microbial community composition at different soil depths during the spring tomato production season in Florida. Soil treatments included ASD using 6.9 m3 ha−1 of molasses with 11 Mg ha−1 of composted poultry litter (CPL) (ASD0.5), ASD with 13.9 m3 ha−1 of molasses and 22 Mg ha−1 CPL (ASD1.0), and chemical soil fumigation (CSF) using a mixture of 1,3-dichloropropene and chloropicrin. Soil microbial community composition was measured at soil depths of 0–15 and 15–30 cm using phospholipid fatty acid (PLFA) analysis at 0, 36, 76, and 99 days after transplanting (DAT). Fatty acid methyl esters were categorized into biomarker groups including total microbial biomass (TMB), G+ bacteria (G+), G− bacteria (G−), actinomycetes (Actino), arbuscular mycorrhizal fungi (AMF), protozoa, and general fungi (F). Soil concentrations of G+, Actino, F, AMF, and the ratio of F:bacteria (B) were significantly impacted by a soil treatment × soil depth × sampling time three-way interaction. All the microbial biomarkers were significantly affected by soil treatment × sampling depth two-way interactions except for protozoa and F:B ratio. Concentrations of TMB, Actino, AMF, F, G+, and G− bacteria were significantly increased in ASD treated soils at both 0–15 and 15–30 cm soil depths across different sampling times compared with CSF. In addition, the concentrations of G+ and G− bacteria, AMF, F, and TMB were higher at 0–15 vs. 15–30 cm soil depth under ASD treatments, whereas no soil depth differences were observed in CSF. Discriminant analysis further confirmed that soil microbial community composition was distinctly different in CSF compared with ASD treatments. The soil microbial profile was well-differentiated between the two soil depths under ASD treatments but not in CSF, while the enhancement of PLFA biomarkers by ASD decreased with increasing soil depth.

Effect of nitrogen application rate under organic and conventional systems on rice (Oryza sativa L.) growth, grain yield, soil properties, and greenhouse gas emissions

The use of appropriate nitrogen (N) rates is important to optimize organic rice yield potential while minimizing environmental impact and input costs. A greenhouse experiment was conducted to identify the optimal N rate for organic and conventional rice and determine its effects on rice yield, soil properties, and greenhouse gas emissions. Six N rates (0, 50, 100, 150, 200, and 250 kg ha−1) and two cropping systems (organic, conventional) were included in this study. Plant dry biomass, panicle number, and yield of conventional rice linearly increased with increasing N rate from 0 to 250 kg ha−1, whereas those of organic rice increased significantly with increasing N rate until 200 kg ha−1. Conventional rice had a significantly taller plant, whereas organic rice had a significantly greater tiller number. At the optimal N rate, the panicle number and yield of organic rice were 77.3% and 92.7% of those of conventional rice, respectively. CO2 and CH4 emissions peaked at the reproductive stage, whereas N2O emissions peaked at the vegetative stage. Global warming potential (GWP) increased with increasing N rate and peaked at 200 and 250 kg N ha−1, respectively, in the organic and conventional system; however, greenhouse gas intensity (GHGI) was not affected by N rate in both systems. Of the measured soil parameters, total microbial biomass (TMB) was significantly correlated to plant growth, yield, and GWP. Our study indicated that the optimal N rate was 200 kg ha−1 for organic rice and 250 kg ha−1 or higher for conventional rice to approach yield potential.

Compost Addition Attenuates the Negative Impacts of High Soil Mineral Nitrogen Levels on Rhizosphere Microbial Characteristics and Enhances Cucumber Growth in Monoculture Systems.

Due to the increase in the human population, it is necessary to seek efficient methods of increasing crop productivity and, simultaneously, sustaining the soil. One way is to grow high demand crops continuously without rotating with other crops. This practice is often accompanied by increased rates of fertilizer application that can affect efficient nitrogen (N) cycling in the plant rhizosphere soil which, in turn, affects both plant growth and environmental pollution. In the present study, twelve various cucumber soils were selected from monoculture systems presenting different cropping years and divided into two groups including soils with relatively high mineral N (HMN) content (N > 100 mg kg−1 soil) and those with a lower mineral N (LMN) content (N < 100 mg kg−1 soil). All soils were amended with the addition of compost alone or in combination with bacterial inoculation to evaluate their effects on plant growth, microbial numbers, N mineralization, and N cycling genes. In general, the HMN soils increased (p < 0.05) net N mineralization (NNM) but did not statistically (p > 0.05) affect plant biomass compared to the LMN soils; however, compost addition increased both NNM and plant biomass in the HMN soils. In addition, the HMN soils had higher fungal pathogen numbers (FPNs) but lower total microbial biomass (TMB) and bacterial numbers (BNs) compared to the LMN soils; however, compost addition decreased FPNs but increased TMB and BNs in the HMN soils (all p < 0.05). Plant biomass was positively related to TMB, BN and NNM but was negatively related to FPN (all p < 0.05). In summary, compost addition reduced the high mineral N levels’ adverse effects on the rhizosphere soil and plant growth.

Effects of common European tree species on soil microbial resource limitation, microbial communities and soil carbon

Studies of tree species effects on soils have revealed a significant impact on soil organic carbon (SOC) stocks and the carbon (C) distribution between forest floor and mineral soil, but the underlying mechanisms including the roles of litter traits, soil properties, and microbiome remain unclear. To address this challenge, we tested the effect of six common European tree species on the quality and nutrient availability of soil organic matter (SOM) as perceived by the naturally assembled microbial communities and explored the possible links between soil enzyme activities (EAs), microbial resource limitation, and microbial community with SOC stocks. The six studied tree species (Acer pseudoplatanus L., Fraxinus excelsior L, Fagus sylvatica L., Quercus robur L., Tilia cordata L., and Picea abies L.) were planted in common garden monocultures more than 40 years ago at six sites across Denmark. In forest floor, microbial biomass C, fungal and total microbial biomass and fungi to bacteria (F/B) ratios decreased with decreasing litter quality. Ecoenzymatic stoichiometry and relative EAs indicated that microbes in spruce forest floor were more limited by phosphorus (P) than in maple, lime, and beech, while microbes in mineral soils were less P limited in spruce than in other monocultures. Mineral soil under the tree species associated with arbuscular mycorrhizal (AM) fungi had higher microbial C and P limitation, bacterial biomass and total microbial biomass than under tree species associated with ectomycorrhizal (EcM) fungi. Our results indicated that tree species with high-quality litter (i.e. AM-associated trees) had (i) higher microbial biomass and less nutrient limitation that were conducive to higher decomposition rates and lower C stocks in the forest floor, and (ii) such tree species could lead to both greater stabilization of mineral soil C by mineral-associated OM formation and greater microbial mineralization of SOM with higher microbial resource demand. The results suggest that tree species-mediated EA, microbial resource limitation and microbial community composition are important drivers of stocks and vertical distribution of SOC among tree species and between the two types of associated mycorrhiza.

Functional trait variation and community-weighted means of tree traits can alter soil microbial biomass and community composition

The interactions between plant diversity and the soil microbial community are crucial for maintaining multiple ecosystem functions. However, the underlying mechanisms of how plant diversity impacts the soil microbial biomass and community composition are still unclear. In this study, we used a biodiversity-ecosystem function experiment to explore whether tree species richness affects the soil microbial biomass and community composition through functional trait variation and community-weighted trait means (CWM). The diversity gradient covered 1, 4, 8, 16 and 32 tree species. Phospholipid fatty acid analysis was used to determine the soil's total microbial biomass and composition. We found that an increase in tree species richness decreased the soil's total microbial biomass, with a more pronounced decrease in young forests with a lower functional trait variation in root nitrogen or with resource-conservative traits (i.e., higher CWM of leaf dry matter content). An increase in tree species richness decreased the biomass ratio of gram-positive to gram-negative bacteria but did not significantly affect the fungi to bacteria ratio. The fungi to bacteria ratio significantly decreased with the CWM of leaf nitrogen content and the functional trait variation in leaf dry matter content. Both the functional trait variation and CWM of the plant leaf and root traits related to resource acquisition influenced the strength and direction of the tree species richness effect on the soil microbial community. Our findings indicated that the functional trait variation and CWM of plant functional traits of the tree communities drive the changes in soil microbial biomass and community composition, which in the long-term feedback on ecosystem functions and services they provide.