David J. Burke

Soil microbial responses to elevated phosphorus and pH in acidic temperate deciduous forests

Although northern temperate forests are generally not considered phosphorus (P) limited, ecosystem P limitation may occur on highly weathered or strongly acidic soils where bioavailable inorganic P is low. In such environments, soil organisms may compensate by increasing the utilization of organic P via the production of extracellular enzymes to prevent limitation. In this study, we experimentally increased available P and/or pH in several acidic eastern deciduous forests underlain by glaciated and unglaciated soils in eastern Ohio, USA. We hypothesized that where inorganic P is low; soil microbes are able to access organic P by increasing production of phosphatase enzymes, thereby overcoming biogeochemical P limitations. We measured surface soil for: available P pools, N mineralization and nitrification rates, total C and N, enzymes responsible for C, N, and P hydrolysis, and microbial community composition (PLFA). Increasing surface soil pH a whole unit had little effect on microbial community composition, but increased N cycling rates in unglaciated soils. Phosphorus additions suppressed phosphatase activities over 60% in the unglaciated soils but were unchanged in the glaciated soils. All treatments had minimal influence on microbial biomass, but available pools of P strongly correlated with microbial composition. Microbes may be dependent on sources of organic P in some forest ecosystems and from a microbial perspective soil pH might be less important overall than P availability. Although our sampling was conducted less than 1 year after treatment initiation, microbial community composition was strongly influenced by available P pools and these effects may be greater than short-term increases in soil pH.

Vegetation and Soil Environment Influence the Spatial Distribution of Root-Associated Fungi in a Mature Beech-Maple Forest

ABSTRACT Although the level of diversity of root-associated fungi can be quite high, the effect of plant distribution and soil environment on root-associated fungal communities at fine spatial scales has received little attention. Here, we examine how soil environment and plant distribution affect the occurrence, diversity, and community structure of root-associated fungi at local patch scales within a mature forest. We used terminal restriction fragment length polymorphism and sequence analysis to detect 63 fungal species representing 28 different genera colonizing tree root tips. At least 32 species matched previously identified mycorrhizal fungi, with the remaining fungi including both saprotrophic and parasitic species. Root fungal communities were significantly different between June and September, suggesting a rapid temporal change in root fungal communities. Plant distribution affected root fungal communities, with some root fungi positively correlated with tree diameter and herbaceous-plant coverage. Some aspects of the soil environment were correlated with root fungal community structure, with the abundance of some root fungi positively correlated with soil pH and moisture content in June and with soil phosphorous (P) in September. Fungal distribution and community structure may be governed by plant-soil interactions at fine spatial scales within a mature forest. Soil P may play a role in structuring root fungal communities at certain times of the year.

Iron Oxide and Titanium Dioxide Nanoparticle Effects on Plant Performance and Root Associated Microbes

In this study, we investigated the effect of positively and negatively charged Fe3O4 and TiO2 nanoparticles (NPs) on the growth of soybean plants (Glycine max.) and their root associated soil microbes. Soybean plants were grown in a greenhouse for six weeks after application of different amounts of NPs, and plant growth and nutrient content were examined. Roots were analyzed for colonization by arbuscular mycorrhizal (AM) fungi and nodule-forming nitrogen fixing bacteria using DNA-based techniques. We found that plant growth was significantly lower with the application of TiO2 as compared to Fe3O4 NPs. The leaf carbon was also marginally significant lower in plants treated with TiO2 NPs; however, leaf phosphorus was reduced in plants treated with Fe3O4. We found no effects of NP type, concentration, or charge on the community structure of either rhizobia or AM fungi colonizing plant roots. However, the charge of the Fe3O4 NPs affected both colonization of the root system by rhizobia as well as leaf phosphorus content. Our results indicate that the type of NP can affect plant growth and nutrient content in an agriculturally important crop species, and that the charge of these particles influences the colonization of the root system by nitrogen-fixing bacteria.

Titanium oxide nanoparticle effects on composition of soil microbial communities and plant performance

We examined the effect of TiO2 nanoparticles (NPs) on the growth of maize and soybean plants and associated soil microbial communities. Plants were grown in a greenhouse, and low levels of undoped or nitrogen-doped TiO2 NPs were applied. Plant growth and nutrient content were determined, and effects of NPs on composition of soil microbial communities were examined using terminal restriction fragment length polymorphism analysis (TRFLP) of rDNA. We found no significant effects of TiO2 NPs on plant growth, nutrient content, or the composition of bacterial communities within the rhizosphere. However, arbuscular mycorrhizal fungal communities were affected by application of undoped and nitrogen-doped TiO2 NPs. This observation may be partially attributed to the small but significant TiO2 NP uptake levels in the root tissues of both plants. Our results suggest that even low concentrations of TiO2 NPs may influence some important groups of soil microbes, such as mycorrhizal fungi, but changes in the composition of microbial communities may not affect plant growth under conditions of adequate moisture and nutrients.

Mycorrhizal Response to Experimental pH and P Manipulation in Acidic Hardwood Forests

Many temperate forests of the Northeastern United States and Europe have received significant anthropogenic acid and nitrogen (N) deposition over the last century. Although temperate hardwood forests are generally thought to be N-limited, anthropogenic deposition increases the possibility of phosphorus (P) limiting productivity in these forest ecosystems. Moreover, inorganic P availability is largely controlled by soil pH and biogeochemical theory suggests that forests with acidic soils (i.e., <pH 5) are particularly vulnerable to P limitation. Results from previous studies in these systems are mixed with evidence both for and against P limitation. We hypothesized that shifts in mycorrhizal colonization and community structure help temperate forest ecosystems overcome an underlying P limitation by accessing mineral and organic P sources that are otherwise unavailable for direct plant uptake. We examined arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) communities and soil microbial activity in an ecosystem-level experiment where soil pH and P availability were manipulated in mixed deciduous forests across eastern Ohio, USA. One year after treatment initiation, AM root biomass was positively correlated with the most available P pool, resin P, while AM colonization was negatively correlated. In total, 15,876 EcM root tips were identified and assigned to 26 genera and 219 operational taxonomic units (97% similarity). Ectomycorrhizal richness and root tip abundance were negatively correlated with the moderately available P pools, while the relative percent of tips colonized by Ascomycetes was positively correlated with soil pH. Canonical correspondence analysis revealed regional, but not treatment, differences in AM communities, while EcM communities had both treatment and regional differences. Our findings highlight the complex interactions between mycorrhizae and the soil environment and further underscore the fact that mycorrhizal communities do not merely reflect the host plant community.

The effects of pH change and NO−3 pulse on microbial community structure and function: a vernal pool microcosm study

Forest vernal pools experience strong environmental fluctuations, such as changes in water chemistry, which are often correlated with changes in microbial community structure. However, very little is known about the extent to which these community changes influence ecosystem processes in vernal pools. This study utilized experimental vernal pool microcosms to simulate persistent pH alteration and a pulse input of nitrate (NO3 -), which are common perturbations to temperate vernal pool ecosystems. pH was manipulated at the onset and microbial respiration was monitored throughout the study (122 days). On day 29, NO3 - was added and denitrification rate was measured and bacterial, fungal, and denitrifier communities were profiled on day 30 and day 31. Microbial respiration and both bacterial and fungal community structure were altered by the pH treatment, demonstrating both structural and functional microbial responses. The NO3 - pulse increased denitrification rate without associated changes in community structure, suggesting that microbial communities responded functionally without structural shifts. The functioning of natural vernal pools, which experience both persistent and short-term environmental change, may thus depend on the type and duration of the change or disturbance.

Spatial heterogeneity of plant–soil feedbacks increases per capita reproductive biomass of species at an establishment disadvantage

Plant–soil feedbacks have been widely implicated as a driver of plant community diversity, and the coexistence prediction generated by a negative plant–soil feedback can be tested using the mutual invasibility criterion: if two populations are able to invade one another, this result is consistent with stable coexistence. We previously showed that two co-occurring Rumex species exhibit negative pairwise plant–soil feedbacks, predicting that plant–soil feedbacks could lead to their coexistence. However, whether plants are able to reproduce when at an establishment disadvantage (“invasibility”), or what drivers in the soil might correlate with this pattern, are unknown. To address these questions, we created experimental plots with heterogeneous and homogeneous soils using field-collected conditioned soils from each of these Rumex species. We then allowed resident plants of each species to establish and added invader seeds of the congener to evaluate invasibility. Rumex congeners were mutually invasible, in that both species were able to establish and reproduce in the other’s resident population. Invaders of both species had twice as much reproduction in heterogeneous compared to homogeneous soils; thus the spatial arrangement of plant–soil feedbacks may influence coexistence. Soil mixing had a non-additive effect on the soil bacterial and fungal communities, soil moisture, and phosphorous availability, suggesting that disturbance could dramatically alter soil legacy effects. Because the spatial arrangement of soil patches has coexistence implications, plant–soil feedback studies should move beyond studies of mean effects of single patch types, to consider how the spatial arrangement of patches in the field influences plant communities.

Mycorrhizal fungal communities respond to experimental elevation of soil pH and P availability in temperate hardwood forests

Many forests are affected by chronic acid deposition, which can lower soil pH and limit the availability of nutrients such as phosphorus (P), but the response of mycorrhizal fungi to changes in soil pH and P availability and how this affects tree acquisition of nutrients is not well understood. Here, we describe an ecosystem-level manipulation in 72 plots, which increased pH and/or P availability across six forests in Ohio, USA. Two years after treatment initiation, mycorrhizal fungi on roots were examined with molecular techniques, including 454-pyrosequencing. Elevating pH significantly increased arbuscular mycorrhizal (AM) fungal colonization and total fungal biomass, and affected community structure of AM and ectomycorrhizal (EcM) fungi, suggesting that raising soil pH altered both mycorrhizal fungal communities and fungal growth. AM fungal taxa were generally negatively correlated with recalcitrant P pools and soil enzyme activity, whereas EcM fungal taxa displayed variable responses, suggesting that these groups respond differently to P availability. Additionally, the production of extracellular phosphatase enzymes in soil decreased under elevated pH, suggesting a shift in functional activity of soil microbes with pH alteration. Thus, our findings suggest that elevating pH increased soil P availability, which may partly underlie the mycorrhizal fungal responses we observed.

Effects of annual and interannual environmental variability on soil fungi associated with an old-growth, temperate hardwood forest

Seasonal and interannual variability in temperature, precipitation and chemical resources may regulate fungal community structure in forests but the effect of such variability is still poorly understood. In this study, I examined changes in fungal communities over two years and how these changes were correlated to natural variation in soil conditions. Soil cores were collected every month for three years from permanent plots established in an old-growth hardwood forest, and molecular methods were used to detect fungal species. Species richness and diversity were not consistent between years with richness and diversity significantly affected by season in one year but significantly affected by depth in the other year. These differences were associated with variation in late winter snow cover. Fungal communities significantly varied by plot location, season and depth and differences were consistent between years but fungal species within the community were not consistent in their seasonality or in their preference for certain soil depths. Some fungal species, however, were found to be consistently correlated with soil chemistry across sampled years. These results suggest that fungal community changes reflect the behavior of the individual species within the community pool and how those species respond to local resource availability.

Seasonal variation in mycorrhizal fungi colonizing roots of Allium tricoccum (wild leek) in a mature mixed hardwood forest

The community of arbuscular mycorrhizal (AM) fungi colonizing roots of the forest herb Allium tricoccum Ait. (wild leek) was examined to assess whether colonization varied seasonally and spatially within the forest. Whole plants were collected to coincide with observed phenological stages, and the perennial tissue (i.e., the bulb) was used to analyze total C, N, and P over the growing season. AM fungal community composition, structure, and abundance were assessed in roots by terminal restriction fragment length polymorphism analysis and quantitative PCR. It was found that A. tricoccum rDNA co-amplified using the general AM primers NS31/AM1, and a new primer for qPCR was designed that discriminated against plant DNA to quantify AM colonization. Community structure of AM fungi did not vary seasonally, but did change spatially within the forest, and AM fungal communities were correlated with the presence of overstory tree species. Fungal colonization of roots, however, did change seasonally with a maximum observed in late winter and early spring following leaf emergence. Maximum AM fungal colonization was associated with declines in bulb N and P, suggesting that leaf emergence and growth were responsible for both declines in stored nutrients and increases in AM fungal colonization. Plant N and P contents increased between late summer and early spring while C contents remained unchanged. The observed increase in nutrient content during a time when A. tricoccum lacks leaves indicates that the roots or AM fungi are metabolically active and acquire nutrients during this time, despite an absence of photosynthesis and thus a direct supply of C from A. tricoccum.