Soil Fungal Abundance Research Articles

Divergence in fungal abundance and community structure between soils under long-term mineral and organic fertilization

Fertilization maintains soil fertility and maximizes crop productivity, but changes soil microbial community structure and functions. However, little is known about the effects of long-term mineral and/or organic fertilization on fungal communities which regulate nutrient cycling and crop growth. The responses of fungal abundance and community structure to 29-year mineral and/or organic fertilization were investigated in Ultisol using quantitative polymerase chain reaction (qPCR) and high-throughput sequencing (Illumina Mi-Seq). Compared to the control, mineral N fertilization decreased fungal abundance by 44%, but showed little effect on crop yield and fungal diversity. The NPK fertilization increased crop yield by 4.5 times and fungal diversity by 1.4 times, but had little effect on fungal abundance relative to the control. Manure application increased crop yield by 8.4 times, fungal abundance by 1.8 times and fungal diversity by 1.5 times relative to the control. Application of manure plus NPK increased crop yield by 9.5 times, fungal abundance by 1.9 times and fungal diversity by 1.6 times relative to the control. Long-term fertilization led to dramatic shifts in fungal community composition. Compared to the control, mineral and organic fertilization decreased the relative abundance of Ascomycota and Basidiomycota, respectively. The fungal community composition diverged between soils with mineral and organic fertilization. Changes in soil organic carbon (SOC) and nutrient contents primarily shifted fungal abundance and community structure. Manure application resulted in higher SOC and nutrient contents, and thus affected fungal abundance and community structure more strongly than mineral fertilization. Manure application rather than mineral fertilization increased the relative abundance of certain favorable fungal taxa (e.g., Pseudaleuria and Hypocreales) which suppress crop pathogens. Overall, long-term manure application explained patterns in soil fertility, crop productivity, fungal abundance, diversity and community composition better than mineral fertilization.

Plant invader alters soil food web via changes to fungal resources.

While aboveground impacts of invasive plants are well documented, their influence on soil food webs remains less understood. Previous research has revealed that bottom-up forces are widespread in soil food webs of woodlands. Thus, an invasive plant that negatively impacts the base of the food web will likely decrease primary consumers as well as their predators. We examined how a North American plant invader, garlic mustard (Alliaria petiolata), affects arthropod primary (springtails and oribatid mites) and secondary (predaceous mites) consumers of the soil food web via changes to fungal resources. We measured the abundances of plants, soil fungi, fungivores, and predators in garlic mustard-invaded and uninvaded 1-m2 plots in five Midwestern USA woodlands. We then conducted a mesocosm (0.25-m2 plots) experiment to tease apart the direct and indirect effects of garlic mustard by manipulating plant identity (garlic mustard vs. native plant), soil history (invaded vs. uninvaded), and fungicide application (fungicide vs. no fungicide). Our first study revealed that plots without garlic mustard had 2.8 and 1.4 × more fungi and fungivores, respectively. Predator densities did not differ. Fungal composition and structural equation modeling (SEM) revealed the garlic mustard effects on fungivores were correlated with fungal declines. The mesocosm experiment confirmed that the impacts were indirect, as fungicide plots harbored similar fungivore densities, whereas fungivore densities differed according to plant identity and soil history in the fungicide-free plots. Our results reveal that by altering soil fungal abundance, an invasive plant can indirectly affect primary consumers in soil food webs, but this indirect effect does not influence predators.

Fungal abundance and diversity as influenced by properties of Technosols developed from mine wastes containing iron sulphides: A case study from abandoned iron sulphide and uranium mine in Rudki, south-central Poland

Reclamation of mine spoils is a process leading to initiation of soil-forming and biological processes in former mining areas. The aim of the present study was to demonstrate the change in soil fungi abundance and diversity depending on Technosols properties as an effect of reclamation in 1970s. The investigation was carried out in the area of the abandoned “Staszic” mine in Rudki village (south-central Poland). Three soil profiles developed from mine wastes were investigated. Basic physicochemical properties and fungal abundance and diversity were determined. The results showed that fungal abundance and species composition is diverse in the studied Technosols, which is closely related to soil properties, in particular with pH, total organic carbon (TOC) and total nitrogen (TN) content. Profile R1 represented a site where reclamation (i.e. neutralization of high acidity) did not succeed, therefore the pH of soil was low (3.0–3.9), plant cover was very scarce, and there was a very low concentration of TOC (up to 0.6%) and TN (up to 0.06%). Profile R1 was the most specific in terms of fungal diversity. The most frequent fungal species was acidophilous Acidiella sp. Profile R2 was located in close vicinity of R1 profile, though it represented a site where neutralization succeeded. Therefore, pH was ~7, and high contents of TOC and TN (up to 8% and 0.65% respectively) occurred in the topsoil of profile R2, whereas the subsoil was acidic (pH 3.9) and poor in TOC and TN. Profile R3 was characterized by high pH (7.2–7.6) throughout the profile, high contents of TOC and TN (up to 4.8% and 0.41% respectively) in the topsoil as well as high concentrations of trace elements (e.g. Pb, Zn, Cu). Our analysis showed that the highest fungal diversity was noted in surface horizons. The study confirmed the distinction of surface horizon of profile R2 and the whole profile R3 in terms of fungal species. High fungal abundance and diversity in R2 and R3 soil profile suggests favourable changes in the mycobiota structure as a result of improvement of soil properties due to reclamation works.

Effect of long‐term mineral fertilisation on soil microbial abundance, community structure and diversity in a Typic Hapludoll under intensive farming systems

AbstractFertiliser application can not only influence plant communities, but also the soil microbial community dynamics, and consequently soil quality. Specifically, mineral fertilisation can directly or indirectly affect soil chemical properties, microbial abundance and, the structure and diversity of soil microbial communities. We investigated the impact of six different mineral fertiliser regimes in a maize/soybean rotation system: control (CK, without fertilisation), PS (application of phosphorus plus sulphur), NS (application of nitrogen plus S), NP (application of N plus P), NPS (application of N, P plus S) and NPSm (application of N, P, S plus micronutrients). Soil samples were collected at the physiological maturity stage of maize and soybean in March of 2013 and 2014, respectively. Overall, mineral fertilisation resulted in significantly decreased soil pH and increased total organic carbon compared with the control (CK). The analysis of terminal restriction fragment length polymorphism (T‐RFLP) revealed that mineral fertilisers caused a shift in the composition of both bacterial and fungal communities. In 2013, the highest value of Shannon diversity of bacterial terminal restriction fragments (TRFs) was found in control soils. In 2014, NPSm treated soils showed the lowest values of diversity for both bacterial and fungal TRFs. In both crop growing seasons, the analysis of phospholipid fatty acid (PLFA) detected the lowest value of total microbial biomass under CK. As PLFA analysis can be used to evaluate total microbial community, this result suggests that fertilisation increased total microbial biomass. When the bacterial and fungal abundance were examined using real time polymerase chain reaction, the results revealed that mineral fertilisation led to decreased bacterial abundance (16S rRNA), while fungal abundance (18S rRNA) was found to be increased in both crop growing seasons. Our results show that mineral fertiliser application has a significant impact on soil properties, bacterial and fungal abundance and microbial diversity. However, further studies are needed to better understand the mechanisms involved in the changes to microbial communities as a consequence of mineral fertilisation.

Improvement effects of quicklime and calcium magnesium phosphate fertilizer on acidified soil cultivating Codonopsis tangshen.

To solve the problem of soil acidification in the cultivation of Codonopsis tangshen, laboratory experiments were carried out to investigate C. tangshen seed germination, seedling growth and soil exchangeable acid, microbial community structure after applying quicklime (QL) and calcium magnesium phosphate fertilizer (CMP). The results showed that QL and CMP treatments significantly improved the survival rate of C. tangshen seedlings from 147.7% to 326.7% and from 270.1% to 311.2%, respectively. The maximum increase rates of the height of C. tangshen seedlings were 516.7% and 546.3%, and that of root length were 798.0% and 679.2% in the treatments of QL and CMP, respectively. 1‰-4‰ QL or CMP treatments increased the relative chlorophyll content, antioxidant enzyme activity and the content of soluble protein of C. tangshen seedlings, decreased the content of malondialdehyde and superoxide anion radical of seedlings, increased soil pH by 0.88-2.02 units and 0.23-1.19 units, and decreased the exchangeable aluminum content in soil by 53.0%-95.3% and 17.6%-81.3%, respectively. Soil bacterial and actinomycetic abundances were significantly higher in 2‰-4‰ QL or CMP treatments than that in the control. Soil fungal abundance was significantly lower in the QL treatment of 2‰ and CMP treatment of 4‰. 1‰-4‰ QL or CMP treatments significantly increased fresh weight of C. tangshen tubers by 40.5%-78.5% and 28.4%-78.8%, respectively. In conclusion, the suitable quantity of QL and CMP for acidified soil (pH=4.12, ρb=1.15 g·cm-3, tillage layer=15 cm) amendment were 1.73-3.45 t·hm-2 and 3.45-6.90 t·hm-2, and QL and CMP amendment could fit the optimum soil pH (5.5-6.5) for the growth of C. tangshen seedlings.

Seasonal Dynamics of Soil Fungal and Bacterial Communities in Cool-Temperate Montane Forests

Both fungal and bacterial communities in soils play key roles in driving forest ecosystem processes across multiple time scales, but how seasonal changes in environmental factors shape these microbial communities is not well understood. Here, we aimed to evaluate the importance of seasons, elevation, and soil depth in determining soil fungal and bacterial communities, given the influence of climate conditions, soil properties and plant traits. In this study, seasonal patterns of diversity and abundance did not synchronize between fungi and bacteria, where soil fertility explained the diversity and abundance of soil fungi but soil water content explained those of soil bacteria. Model-based clustering showed that seasonal changes in both abundant and rare taxonomic groups were different between soil fungi and bacteria. The cluster represented by ectomycorrhizal genus Lactarius was a dominant group across soil fungal communities and fluctuated seasonally. For soil bacteria, the clusters composed of dominant genera were seasonally stable but varied greatly depending on elevation and soil depth. Seasonally changing clusters of soil bacteria (e.g., Nitrospira and Pelosinus) were not dominant groups and were related to plant phenology. These findings suggest that the contribution of seasonal changes in climate conditions, soil fertility, and plant phenology to microbial communities might be equal to or greater than the effects of spatial heterogeneity of those factors. Our study identifies aboveground–belowground components as key factors explaining how microbial communities change during a year in forest soils at mid-to-high latitudes.

Recurrent fires do not affect the abundance of soil fungi in a frequently burned pine savanna.

While the negative effects of infrequent, high-intensity fire on soil fungal abundance are well-understood, it remains unclear how the short-term history of frequent, low-intensity fire in fire-dependent ecosystems impacts abundance, and whether this history governs any abundance declines. We used prescribed fire to experimentally alter the short-term fire history of patches within a fire-frequented old-growth pine savanna over a 3 y period. We then quantified fungal abundance before and after the final fire using phospholipid fatty acid (PLFA) assays and Droplet Digital™ PCR (ddPCR). Short-term fire history largely did not affect total fungal abundance nor pre- to post-fire abundance shifts. While producing similar conclusions, PLFA and ddPCR data were not correlated. In addition to piloting a new method to quantify soil fungal abundance, our findings indicate that, within fire-frequented pine savannas, recurrent fires do not consistently decrease total fungal abundance, and abundance changes are not contingent upon short-term fire history. This suggests that many fungi in fire-dependent ecosystems are fire-tolerant.

Significant alterations in soil fungal communities along a chronosequence of Spartina alterniflora invasion in a Chinese Yellow Sea coastal wetland.

Plant invasion typically alters the microbial communities of soils, which affects ecosystem carbon (C) and nitrogen (N) cycles. The responses of the soil fungal communities to plant invasion along its chronosequence remain poorly understood. For this study, we investigated variations in soil fungal communities through Illumina MiSeq sequencing analyses of the fungal internal transcribed spacer (ITS) region, and quantitative polymerase chain reaction (qPCR), along a chronosequence (i.e., 9-, 13-, 20- and 23-year-old) of invasive Spartina alterniflora. We compared these variations with those of bare flat in a Chinese Yellow Sea coastal wetland. Our results highlighted that the abundance of soil fungi, the number of operational taxonomic units (OTUs), species richness, and Shannon diversity indices for soil fungal communities were highest in 9-year-old S. alterniflora soil, which gradually declined along the invasion chronosequence. The relative abundance of copiotrophic Basidiomycota revealed significant decreasing trend, while the relative abundance of oligotrophic Ascomycota gradually increased along the S. alterniflora invasion chronosequence. The relative abundance of soil saprotrophic fungi (e.g., undefined saprotrophs) was gradually reduced while symbiotic fungi (e.g., ectomycorrhizal fungi) and pathotrophic fungi (e.g., plant and animal pathogens) progressively increased along the S. alterniflora invasion chronosequence. Our results suggested that S. alterniflora invasion significantly altered soil fungal abundance and diversity, community composition, trophic modes, and functional groups along a chronosequence, via substantially reduced soil litter inputs, and gradually decreased soil pH, moisture, and soil nutrient substrates along the invasion chronosequence, from 9 to 23 years. These changes in soil fungal communities, particularly their trophic modes and functional groups along the S. alterniflora invasion chronosequence could well impact the decomposition and accumulation of soil C and N, while potentially altering ecosystem C and N sinks in a Chinese Yellow Sea coastal wetland.

Continuous cropping of soybean alters the bulk and rhizospheric soil fungal communities in a Mollisol of Northeast PR China

AbstractContinuous cropping of soybean causes soil degradation and decreased soybean yield in Northeast PR China. However, the mechanism underlying the effect on soil fungal communities and the relationship between these effects and cropping systems have not yet been fully elucidated. In this study, we comparatively investigated the abundance, diversity, and structures of fungal communities in the bulk and rhizospheric soils of soybean grown in two cropping systems, that is, continuous cropping (CC) of soybean and cropping rotation (CR) with maize using real‐time Polymerase Chain Reaction (PCR) and Illumina MiSeq sequencing methods. The results showed that the rhizospheric soil fungal abundance was significantly higher in CC than in CR, but the opposite trend was observed in bulk soils. CC decreased the fungal alpha diversity in both bulk and rhizospheric soils compared with CR. The fungal community compositions were distinctly different between CC and CR in both bulk and rhizospheric soils, and the composition and diversity in bulk soils were predominantly affected by the soil carbon to nitrigen (C/N) ratio. The soil fungal functional groups varied between the two cropping systems; CC increased the relative abundances of the potentially pathogenic fungi Fusarium oxysporum and Lectera longa and beneficial fungi Mortierella sp. and Paecilomyces lilacinus. In contrast, CR increased the relative abundance of Ustilago maydis, which is a pathogen that causes corn smut. Our findings showed that CC increased the abundances of plant pathogens, which is harmful to soybean growth; in contrast, the abundances of some beneficial fungi also increased, which suggested that suppressive soils might be developed after long‐term CC.

Soil fungal communities vary with invasion by the exotic Spartina alternifolia Loisel. in coastal salt marshes of eastern China

Soil fungal communities play a critical role in ecosystem carbon (C) and nitrogen (N) cycling. Although the effect of plant invasions on ecosystem C and N cycling is well established, its impact on soil fungal communities is not fully understood. The objective of this study was therefore to understand the variations in soil fungal communities as affected by plant invasion, and the mechanisms that drive these changes. We examined the impacts of invasive Spartina alternifolia Loisel. (SA) on soil fungal abundance, diversity, community composition, trophic modes and functional groups in comparison with bare flat (BF) and native Suaeda salsa (Linn.) Pall. (SS), Scirpus mariqueter Tang et Wang (SM), and Phragmites australis (Cav.) Trin. ex Steud. (PA) communities in coastal salt marshes of eastern China, based on analyses of the quantitative polymerase chain reaction (qPCR) and Illumina MiSeq DNA sequences of fungal internal transcribed spacer (ITS) region. SA invasion increased the soil fungal abundance and diversity compared to BF, SS, SM, and PA soils. The increased soil fungal abundance and diversity were highly related to soil organic carbon (C) and nitrogen (N), water-soluble organic carbon (WSOC), litter C:N ratio, and root C:N ratio. Soil fungal community composition was shifted following SA invasion. Specifically, SA invasion significantly enhanced the relative abundance of Basidiomycota, and reduced the relative abundance of Ascomycota compared with BF, SS, SM, and PA soils. Additionally, SA invasion changed soil fungal trophic modes and functional groups. The relative abundance of saprotrophic fungi significantly increased, while the relative abundances of symbiotic and pathotrophic fungi decreased following SA invasion. Our data revealed that SA invasion altered soil fungal abundance, diversity, community composition, trophic modes and functional groups, which were primarily driven by the quality and quantity of plant residues, soil nutrition substrates, as well as soil physicochemical properties. The changes in soil fungal communities, especially their trophic modes and functional groups following SA invasion would greatly affect soil C and N decomposition and accumulation with potential feedback on climate change.

Effects of biochar amendment and nitrogen fertilization on soil microbial biomass pools in an Alfisol under rain-fed rice cultivation

Field studies were conducted over 2 years to determine the response of soil microbial biomass pool to biochar and N fertilizer combinations in a rain-fed rice cropping system. Biochar was applied at four doses: 0 t ha−1, 3 t ha−1, 6 t ha−1 and 12 t ha−1 in combination with N fertilizer at four rates: 0 kg ha−1, 30 kg ha−1, 60 kg ha−1 and 90 kg ha−1 to a Typic Paleustalf Alfisol. Soil samples from two depths (0–10 and 10–20 cm) were collected to determine microbial biomass C (MBC), N (MBN), P (MBP), MBC/N ratio, MBC/P ratio, soil CO2 flux, microbial qCO2, cultivable bacterial and fungal abundance. Biochar and N fertilizer combination effects on MBC, MBN and MBP pools were dependent on biochar doses, N fertilizer rates and soil depth. MBC/N and MBC/P ratios were decreased after 2 years. Soil CO2 flux was maximum at post-seeding stage of rice plant, while decreasing trends occurred at active tillering and harvest stage. Increasing doses of biochar irrespective of its combination with N fertilizer rates decreased CO2 flux and microbial qCO2. Combinations of biochar and N fertilizer increased fungal/bacterial ratio and induced a shift to a more fungal-dominated population after 2 years. Our results suggest that combination of biochar doses (3–12 t ha−1) with N fertilizer rates had stimulatory effects on microbial biomass pools and activity with positive implications for organic carbon accumulation, nitrogen (N) and phosphorus (P) retention in tropical soils.

Effects of different long-term farmland mulching practices on the loessial soil fungal community in a semiarid region of China

The Northwest Loess Plateau is a typical area of dryland agricultural production in China. Farmland mulching is often used to preserve the soil moisture and increase crop yields. However, the impacts of long-term farmland mulching practices on the soil fungal communities in the loessial soil in semiarid areas of China were less explored. Thus, we investigated the variations in the soil fungal communities under different mulching patterns using high-throughput sequencing to understand how different mulching practices affect these communities. The following treatments were investigated: ridge-furrow mulching pattern (R), flat plastic film mulching (P), flat biodegradable film mulching (B), flat straw mulching (S), and conventional flat planting without mulching as a control (CK). Farmland mulching practices significantly affected the soil fungal diversity and community structure by changing the soil properties. Compared with CK, the P and S treatments significantly increased the soil fungal diversity, thereby suggesting that these practices provided the most suitable growth environment for fungi. The soil moisture and nitrate nitrogen (NO3-N) content were the most important factors that affected the fungal diversity. Nonmetric multidimensional scaling ordination showed that the fungal communities in CK were separated from those in R and B treatments and closely clustered with the communities in the P and S treatments, thereby suggesting that the fungal community compositions differed slightly between the P and S treatments and the CK treatment, but the soil fungal community compositions in the R and B treatments differed significantly from that in CK. In addition, the fungal community composition depended primarily on the soil temperature and NO3-N. These results indicate that different farmland mulching practices affected the soil moisture, soil temperature, and NO3-N to change the soil fungal community distribution patterns in this region. Overall, the soil fungal diversity and abundance were both higher in the P treatment than the other treatments. Therefore, flat plastic film mulching is recommended for semiarid areas.

The interactions between soil microbes and microbial feeding nematodes correlate with fruit productivity of Illicium verum Hook

Soil biodiversity regulates ecosystem structure and functioning through changing biomass, activity, community composition and interactions among soil biota. This study aimed to explore the relationships between soil food webs, soil properties and fruit productivity in plantations of Chinese star anise (Illicium verum Hook). We anticipated that this comparison would allow us to identify key indicators of soil ecosystem associated with fruit yield. We found that soil microbial biomass carbon (MBC), soil microbial biomass nitrogen (MBN), bacterial abundance (B) and fungal abundance (F) derived from phospholipid fatty acid profiling, bacteriovores abundance (Ba), fungivores abundance (Fu) and F/B ratio were resilient to fruit productivity. By contrast, MBC: MBN ratio, total nematode abundance, F/Fu and the correlation between F/B, Fu/Ba and Fu/(Ba+Fu) were responsive to fruit productivity. In conclusion, MBC: MBN and trophic linkages in the detritus food web are important determinants of ecosystem functioning at local scale. Very small change in community composition or interactions among components within soil food webs could disturb some ecosystem processes and ultimately affect plant's productivity. Therefore, we can enhance ecosystem functioning using management practice which is conducive to restore the community composition of soil biota and interactions among components within soil food webs to those of adjacent healthy natural ecosystem.

Preplant Soil Incorporation of Compost to Mitigate Replant Disease: Soil Biological Factors Associated with Plant Growth Promotion in Orchard Soil

Preplant soil incorporation of compost has previously shown potential to suppress Pratylenchus penetrans populations and improve replant establishment of newly planted fruit trees at old orchard sites. Using a greenhouse experiment, we evaluated the effects of preplant incorporation of three compost amendments (agricultural waste compost, yard trimmings compost, and municipal waste compost) on growth of apple seedlings, P. penetrans populations, microbial populations associated with soil suppressiveness, and microbial activity using soil collected from three orchard sites. We also aimed to identify the biological factors that were most strongly associated with enhanced plant growth in compost-amended soil. In four out of nine compost type × soil combinations, compost improved apple seedling growth relative to the control. In four out of nine compost type × soil combinations, compost reduced P. penetrans root infestation relative to the control, and in one compost type × soil combination, compost amendment increased P. penetrans root infestation. Composts stimulated soil microbial activity and abundance, resulting in greater populations of Pseudomonas spp. in soil in seven of the nine compost type × soil combinations. In a step-wise multiple linear regression, P. penetrans root infestation and the total abundance of fungi in soil accounted for the most variance in plant biomass, with increases in both variables correlated with reduced seedling biomass. Overall, composts show variability in the capacity to promote the establishment of fruit trees in orchard soil. Future research should be directed toward understanding variability in compost-induced plant growth promotion among different orchard soils and compost types.

Slash-and-Burn Practices Decrease Arbuscular Mycorrhizal Fungi Abundance in Soil and the Roots of Didierea madagascariensis in the Dry Tropical Forest of Madagascar

Deforestation and the use of fire to clear land have drastic effects on ecosystem functioning and compromise essential ecosystem services, especially in low-income tropical countries such as Madagascar. We evaluated the effects of local slash-and-burn practices on soil nutrients and arbuscular mycorrhizal (AM) fungi abundance in a southwestern Madagascar forest. Nine sampling plot pairs were established along the border of a reserve within the Fiherenana–Manombo (pk-32) complex, where soil and seedling root samples of the endemic tree Didierea madagascariensis were taken. We analysed soil extractable PO43−, NH4+, and NO3− as well as total soil carbon and nitrogen. We analysed AM fungal abundance in soil and roots through fatty acid marker analysis (NLFA and PLFA 16:1ω5), spore extraction, and root staining. Slash-and-burn caused an increase in pH and doubled the plant available nutrients (from 7.4 to 13.1 µg PO43− g−1 and from 6.9 to 13.2 µg NO3− g−1). Total C and total N increased in deforested soil, from 0.6% to 0.84% and from 0.06% to 0.08%, respectively. There was a significant decline in AM fungi abundance in soil, with a decrease in soil NLFA 16:1ω5 from 0.2 to 0.12 nmol/g. AM fungi abundance in D. madagascariensis roots was also negatively affected and colonization decreased from 27.7% to 16.9% and NLFA 16:1ω5 decreased from 75.7 to 19 nmol/g. Together with hyphal network disruption, increased nutrient availability caused by burning is proposed as an explanation behind AM decline in soil and roots of D. madagascariensis. This is the first study to report the effects of slash-and-burn on AM symbiosis in Madagascar’s dry forests, with likely implications for other tropical and subtropical dryland forests worldwide where slash-and-burn is practiced.

Rhizosphere microbial communities of canola and wheat at six paired field sites

Plant physical and chemical characteristics are known to alter rhizosphere microbial communities, but the effect of introducing canola (Brassica napus L.) into monoculture wheat (Triticum aestivum L.) rotations is not clear. Results from a field study in eastern Washington showed that winter canola (WC) influenced the bulk soil microbial community and differentiated it from the community associated with winter wheat (WW). Abundance of soil fungi, including mycorrhizae, was reduced with the introduction of WC. The objective of this research was to determine the differences and similarities in the rhizosphere microbial communities of WC and WW. Canola and wheat rhizosphere soil was collected from six dryland farms in Adams and Douglas Counties, WA. Each farm was a paired site with WC and WW grown in adjacent fields of the same soil type, landscape orientation, and crop history. Canola, or any non-cereal crop, had never been grown previously at the experimental sites. Rhizosphere microbial biomass and community composition, determined using phospholipid fatty acid analysis (PLFA), revealed differences associated with landscape position at the initial fall sampling when WC and WW were in the rosette and tiller development stages, respectively. However, data from spring samples, when WC and WW were in the early bolting and stem elongation growth stages, respectively, showed significant differences in microbial communities between WC and WW rhizosphere soils. Data suggest that initial (fall) microbial community composition were an artifact of previous histories of monocrop wheat production and varied with expected differences in landscape position. As the crops developed, microbial communities became more dissimilar and were differentiated by crop species. Our results show that WC can have significant effects on rhizosphere microbial biomass of specific microbial groups and community structure in wheat-based cropping systems, such as reductions in fungi and gram+ bacteria in some locations. Crop-related changes in the abundance of specific rhizosphere microbial groups may play a key role in the yield of subsequent crops, and overall soil health and nutrient turnover.

Impact of slope exposure on chemical and microbiological properties of Norway spruce deadwood and underlying soil during early stages of decomposition in the Italian Alps

Mountain forest ecosystems are particularly sensitive to changing environmental conditions that affect the rate of deadwood decay and, thus, also soil carbon turnover and forest productivity. Little is known about how slope exposure and climate influence microbial abundance and activity in general, and wood-inhabiting bacteria during deadwood decomposition in particular. Therefore, a field experiment using open mesocosms was carried out along an altitudinal gradient (from 1200 to 2000 m above sea level) in the Italian Alps to evaluate the impact of exposure (north (N)- vs. south (S)-facing sites) on microbial biomass (double stranded DNA, dsDNA); microbial abundance (real-time PCR-based: fungi; dinitrogen reductase, nifH; ammonia-monooxygenase, amoA); and several hydrolytic enzyme activities involved in the main nutrient cycles during decomposition of Picea abies wood blocks (2 × 5 × 5 cm) over a 2-year period. In addition, soil physico-chemical and (micro)biological properties were determined at each site. The cooler, moister and more acidic conditions at north-facing slopes led to an increase in the wood and soil fungal abundance. Furthermore, soil nitrogen-related bacterial functional genes (nifH and amoA) gave a contrasting response to exposure in terms of abundance: nifH (N > S, altitude and decay time-dependent); ammonia-oxidising bacteria (AOB; S > N, altitude and decay time-dependent); ammonia-oxidising archaea (AOA; N > S, only at 2000 m a.s.l.). The AOB and AOA abundance, however, was below the detection limit in the wood blocks. Soil microbial biomass was in general higher at the north-facing slopes, whereas in the wood exposure affected to a lesser extent the microbial biomass. Overall, the exposure-effect on the microbial biomass and abundance as well as for most of the enzymatic activities was altitude- and decay time-dependent.

Urban mycorrhizas: predicting arbuscular mycorrhizal abundance in green roofs

Abstract Mycorrhizas face unique anthropogenic stressors in urban environments, but the factors influencing their abundance in cities remains comparatively unstudied. Using green roofs as a model system, we built a conceptual model outlining the biotic and abiotic factors influencing arbuscular mycorrhizal (AM) fungal abundance in cities. We then tested this model and its multiple causal hypotheses with structural equation modeling using plant, soil, and AM fungal abundance measurements from 60 plots across 12 green roofs in Chicago, USA. The best direct predictor of AM fungal abundance was not plant cover, plant richness, or soil nutrients, but instead green roof age, suggesting temporal accumulation of AM fungal propagules in degraded urban environments. Soil P had the strongest total effect on AM fungal abundance both directly and via indirect promotion of plant cover. This study highlights knowledge gaps and challenges to studying the urban ecology of AM fungi.

DNA Template Dilution Impacts Amplicon Sequencing-Based Estimates of Soil Fungal Diversity

Next generation sequencing of taxonomically relevant marker genes has enabled researchers to sample the richness, diversity, and composition of environmental microbiomes at previously unattainable depths. However, molecular methods may have unintended downstream consequences and the inadvertent undersampling of microbial communities may be a significant pitfall in microbiome profiling. One such procedure, dilution of the DNA template prior to polymerase chain reaction (PCR), may improve marker gene amplification by reducing chimeric read formation and decreasing PCR inhibitor concentrations. However, dilution unavoidably reduces target DNA template number per sample. We evaluated the effects of pre-PCR DNA template dilution on estimates of soil fungal microbiome diversity, composition, and species abundance distributions across a collection of 144 agricultural soil samples. Fungal DNA templates were serially diluted at 0-, 10-, 100-, and 1,000-fold and sequence data of diluted templates were compared with those of an identical set of undiluted templates. For three prairie soil samples, in addition to evaluating variation among replicates of individual samples, we serially diluted fungal DNA extracts from soil samples in triplicate and sequenced undiluted and diluted samples. DNA template dilution significantly reduced estimates of fungal richness and diversity, as compared with undiluted samples. Dilution of DNA template also resulted in reduced relative abundances of rare operational taxonomic units (OTUs) and increased relative abundances of common OTUs. Collectively, changes in OTU abundance distributions following dilution produced substantial shifts in overall fungal community composition. Our results highlight risks associated with sample dilution and point to the potential utility of quantifying pre-PCR template concentration in the estimation of microbiomes. We urge researchers to thoroughly document methods and to reconsider routine dilution of pre-PCR DNA templates particularly for low abundance microbiome samples. As efforts to profile environmental microbiomes using molecular sequencing approaches accelerate, developing an adequate understanding of potential methodological bottlenecks will increase our ability to accurately characterize and compare datasets.

Soil fungal abundance and plant functional traits drive fertile island formation in global drylands

Abstract Dryland vegetation is characterized by discrete plant patches that accumulate and capture soil resources under their canopies. These “fertile islands” are major drivers of dryland ecosystem structure and functioning, yet we lack an integrated understanding of the factors controlling their magnitude and variability at the global scale. We conducted a standardized field survey across 236 drylands from five continents. At each site, we measured the composition, diversity and cover of perennial plants. Fertile island effects were estimated at each site by comparing composite soil samples obtained under the canopy of the dominant plants and in open areas devoid of perennial vegetation. For each sample, we measured 15 soil variables (functions) associated with carbon, nitrogen and phosphorus cycling and used the relative interaction index to quantify the magnitude of the fertile island effect for each function. In 80 sites, we also measured fungal and bacterial abundance (quantitative PCR) and diversity (Illumina MiSeq). The most fertile islands, i.e. those where a higher number of functions were simultaneously enhanced, were found at lower elevation sites with greater soil pH values and sand content under semiarid climates, particularly at locations where the presence of tall woody species with a low‐specific leaf area increased fungal abundance beneath plant canopies, the main direct biotic controller of the fertile island effect in the drylands studied. Positive effects of fungal abundance were particularly associated with greater nutrient contents and microbial activity (soil extracellular enzymes) under plant canopies. Synthesis. Our results show that the formation of fertile islands in global drylands largely depends on: (1) local climatic, topographic and edaphic characteristics, (2) the structure and traits of local plant communities and (3) soil microbial communities. Our study also has broad implications for the management and restoration of dryland ecosystems worldwide, where woody plants are commonly used as nurse plants to enhance the establishment and survival of beneficiary species. Finally, our results suggest that forecasted increases in aridity may enhance the formation of fertile islands in drylands worldwide.