Hyphal length rarely, if ever, decreases. In addition, preliminary evidence indicates that soil organic matter associated with mycorrhizal hyphae might become more prevalent. However, few data exist regarding changes in life span or decomposition rate under CO# enrichment, and these processes have strong controls over the long-term accumulation of soil organic matter pools over time. In addition, shifts in community composition of mycorrhizal fungi with CO# concentration might affect all aspects of mycorrhizal C cycling in an unforeseeable manner. Additional research on ecosystem-level responses and underlying mechanisms is critical.Elevated CO# often occurs concurrently with several other aspects of global change, including widespread N deposition. Increasing N availability might reduce investment by plants in mycorrhizal fungi. This response is especially likely for ECM fungi, as this group acts as an important mechanism of N acquisition for plants . The decline in abundance of fruiting bodies of ECM fungi in European forests has been well documented , and N deposition is considered a major contributing factor. Nitrogen fertilization has often been used to simulate effects of N deposition, and usually produces decreases in mushroom production . This decline in fruiting bodies might in itself represent a noteworthy decrease in ECM fungal biomass,10 plastic plant pots but might not necessarily be accompanied by a decrease in the presence of below-ground tissue . Extraradical hyphae can also account for a substantial portion of mycorrhizal biomass, and ecosystem-level responses of hyphae to N fertilization vary .

For example, the incidence of ECM biomass in root tips was not affected by long-term fertilization in P. ponderosa seedlings or in a Picea abies forest . In AM fungi, Klironomos et al. reported a significant reduction in hyphal length associated with Populus tremuloides saplings after 14 months of N additions, but Eom et al. observed an increase in biomass in a tallgrass prairie fertilized for 10 yr. Of these four studies, all but Karen & Nylund included both live and dead hyphae in their measurements of biomass. These inconsistencies in N response could be attributable to the initial N status of the systems, and to varying influences of alterations in growth rate, decomposition, life span or community structure. Nitrogen treatments also have inconsistent effects on hyphal growth rate . Arnebrant documented significant decreases in growth with increasing N availability in five ECM isolates.However, in another ECM experiment Wallander et al. found no significant N effect on growth rates of four isolates of P. involutus collected from regions exposed to varying levels of N deposition. Aside from these two studies, few direct assessments of N effects on ECM or AM growth rates are reported in the literature. In experiments that have measured ECM biomass after weeks or months of growth, decreases ; lack of response ; or increases under higher N availability have each been observed. Likewise, the responses of AM biomass to N concentration have been positive , negative , or not significant . Much of the inconsistency in N effects among and within studies might be due to variation in responses among mycorrhizal groups or among plant} fungal combinations. Wallander and Nylund reported that S. bovinus was more sensitive to N additions than was Laccaria bicolor when both were grown on Pinus sylvestris in a semi-hydroponic medium. In a microcosm experiment conducted by Arnebrant , two isolates of P. involutus, one isolate of S. bovinus, and two additional unidentified species of ECM fungi were exposed to increasing N availability. The growth rate of S. bovinus and one unknown species declined markedly, while one P. involutus isolate was only slightly affected.

In a separate study by Wallander et al. , four isolates of P. involutus and two of S. bovinus grown in culture also displayed different sensitivities to N additions. One P. involutus isolate from a low-N deposition site, another from a moderate-N site, and an isolate of S. bovinus from a low-N site each grew significantly more slowly when supplied with excess N. Additional isolates from moderate- to high-N sites had no significant response. These N effects were not consistent with those of the seedling experiment, in which hyphal growth rates were not affected in any group. Nevertheless, these three studies suggest that ECM fungi might differ in productivity under N deposition, and that S. bovinus appears particularly susceptible. It remains to be seen whether AM groups might vary as well.Several studies have detailed changes caused by N deposition or fertilization in the species assemblage of mushrooms . However, as the community composition of ECM fruiting bodies can differ from that of below-ground ECM structures , and below-ground biomass could be a substantial C pool, this review focuses on the species composition of fungal structures in the soil. In both a Swedish Picea abies forest and a Scottish Sitka spruce plantation , frequencies of ECM morphotypes on root tips shifted upon long-term N fertilization. Likewise, in Pinus sylvestris forests in Sweden, colonization of ‘bait’ seedlings by one particular morphotype was less frequent in Nfertilized than in control plots . Composition of AM communities can also shift with N availability. In a natural N deposition gradient in southern California coastal sage scrub, spores of Scutellospora and Gigaspora species became less prevalent with increasing deposition. Conversely, spores of certain Glomus species proliferated under the same conditions .

In addition, in tall grass prairie the abundance of spores from Gigaspora gigantea and Glomus mosseae increased with N fertilization, while that of Entrophospora infrequens declined significantly . Johnson noted an increase in the presence of Gigaspora gigantea, Gigaspora margarita, Scutellospora calospora and Glomus occultum, and a decrease in Glomus intraradix after 8 yr fertilization with a suite of nutrients including N and P. Alterations in the species assemblage of mycorrhizal fungi, either directly through N availability or indirectly through shifts in plant communities, appear to be a likely outcome of widespread N deposition.Nitrogen effects on the survivorship and decomposition of mycorrhizal hyphae have received little attention. Using minirhizotrons, Majdi & Nylund found that N fertilization significantly reduced the life span of ectomycorrhizal short roots from 240 to 210 d in a 30-yr-old Norway spruce stand in southwest Sweden. The authors did not speculate on mechanisms underpinning this change, but we suggest that alterations of the ECM community could have been one factor. In another minirhizotron experiment, Rygiewicz et al. recorded no effect of N fertilization on the length of time between appearance and disappearance of ECM tips. This latter result includes both life span and decomposition rate of the fungal tissue. These studies present valuable information on the dynamics of mycorrhizal root tips. However,plastic pots large alterations in turnover of extraradical ECM and AM hyphae by N additions have yet to be reported in the literature. Nitrogen concentrations of hyphae from one P. involutus isolate were reported to increase with higher N availability in a culture experiment, with possible shifts in decomposition rate. Additionally, root turnover can increase with N fertilization , and this response could produce a corresponding decrease in the life span of ECM structures such as mycorrhizal root tips and rhizomorphs.Increases in N availability inconsistently affect hyphal dynamics .

In field studies, this variation in response could be partially attributable to the initial N status of the ecosystem; N-limited systems might respond differently from systems in which another factor limits primary productivity. Nutrient limitation of plants is an important consideration because mycorrhizal fungi derive the majority of their C from the host. However, this possibility has not been explicitly tested. At this point we can only suggest that C storage in living and recently dead mycorrhizal tissue might only be affected in certain systems exposed to N deposition. Furthermore, in glasshouse or culture studies the use of different fungal species or isolates might contribute to conflicting responses of hyphal growth or biomass. Overall, alteration in the community composition of mycorrhizal fungi appears to be the most general response to N addition. Because mycorrhizal groups can vary in chitin content and growth rate, these shifts could have important consequences for C immobilization in live hyphal tissue or its residual soil organic matter. However, a more complete understanding of differences in tissue quality and physiology among groups is necessary in order to predict their influence on C dynamics.Roots are not only vital for anchorage and for acquisition of water and nutrients from the soil, but are also engaged in complex physical and chemical interactions with the soil. Plant roots release approximately 11–40% of their photosynthetically fixed carbon, commonly known as root exudates, into the soil . Root exudates and mucilage act as nutrient sources and as signaling molecules for soil microorganisms, thus shaping the microbial community in the immediate vicinity of the root system . In turn, microbial processes promote plant growth by aiding in nutrient acquisition, plant growth hormone production and bio-control of plant pathogens . The physicochemical characteristics of the surrounding soil are also affected by interactions between roots and the microbial community. This interplay between the different rhizosphere components is affected by spatio-temporal processes, which culminates in dynamic feedback loops that maintain the complex rhizosphere environment with physical, chemical and biological gradients that are distinct from the bulk soil . Understanding these intricate rhizosphere relationships is vital in devising strategies to increase plant productivity and comprehend localized biogeochemical processes. In many rhizosphere studies, the use of pots and containers is predominant as it allows the plants to be cultivated under controlled conditions and at low cost. Compared to field studies, growth of plants in defined spaces also offers advantages in ease of handling, monitoring and sampling . Much of what we know of the rhizosphere microbiome has resulted from such pot-grown plants. However, since the rhizosphere and roots are still out of view in the soil, destructive sampling of the root is required prior to analysis. Destructive sampling may result in the loss of three-dimensional spatial information on rhizosphere processes over time, which is increasingly being recognized as a critical parameter. On the other hand, soil free techniques such as hydroponics and aeroponics can provide visual access to the rhizosphere circumventing the need for destructive sampling. Other alternatives are gel-based substrates which can maintain rhizosphere transparency as well as the 3D architecture of roots and have been applied successfully in high throughput imaging, phenotyping and trait mapping platforms . Nonetheless, the root phenotype and traits of plants grown under soil-free conditions are known to differ from those of soil-grown plants . These soil substitutes do not also accurately simulate the heterogeneous nature of soil aggregates, thus complicating extrapolations for field relevance. Sophisticated imaging approaches such as magnetic resonance imaging and X-ray computer tomography can be used to analyze root systems in the soil with minimal disturbance but they are low throughput, expensive and may not be easily accessible . It is apparent that structural changes in design catered to solving specific challenges in the rhizosphere are indeed necessary. To overcome these challenges relating to the rhizosphere in soil, specialized plant growth chamber systems have been designed, and successful implementation has led to multiple variations of similar designs. These specialized systems often have a visible rhizosphere which enables coupling with other technologies thereby increasing the breadth of experimental techniques applicable to the rhizosphere system. This review discusses representative growth chamber systems designed to study major rhizosphere processes and interactions in soil. Growth platforms resembling conventional containers such as pots and tubes are not covered. Specifically, the reviewed growth systems are selected based on the following criteria: the growth chamber is amenable for use with soil/soil-like substrates and therefore, hydroponics, aeroponics and agar/gel-based systems are not discussed except in microfluidic-based platforms, it is built with the intention to maintain growth of the plant and has architectural features distinct from conventional pots, and lastly it is able to be set up in a laboratory; i.e., field measurement systems and observation platforms are not included. For instance, a minirhizotron, consisting of a camera mounted in a glass tube submerged in the soil which provides non-destructive root imaging over time will not be discussed as it is out of the scope of this review.