Although it is generally accepted that plant community composition is key for predicting rates of ecosystem processes in the face of global change, microbial community composition is often ignored in ecosystem modeling. To address this issue, we review recent experiments and assess whether microbial community composition is resistant, resilient, or functionally redundant in response to four different disturbances. We find that the composition of most microbial groups is sensitive and not immediately resilient to disturbance, regardless of taxonomic breadth of the group or the type of disturbance. Other studies demonstrate that changes in composition are often associated with changes in ecosystem process rates. Thus, changes in microbial communities due to disturbance may directly affect ecosystem processes. Based on these relationships, we propose a simple framework to incorporate microbial community composition into ecosystem process models. We conclude that this effort would benefit from more empirical data on the links among microbial phylogeny, physiological traits, and disturbance responses. These relationships will determine how readily microbial community composition can be used to predict the responses of ecosystem processes to global change.

https://www.pnas.org/content/pnas/105/Supplement_1/11512.full.pdf

Resistance, resilience, and redundancy in microbial communities

This review focuses on some important and challenging aspects of soil extracellular enzyme research. We report on recent discoveries, identify key research needs and highlight the many opportunities offered by interactions with other microbial enzymologists. The biggest challenges are to understand how the chemical, physical and biological properties of soil affect enzyme production, diffusion, substrate turnover and the proportion of the product that is made available to the producer cells. Thus, the factors that regulate the synthesis and secretion of extracellular enzymes and their distribution after they are externalized are important topics, not only for soil enzymologists, but also in the broader context of microbial ecology. In addition, there are many uncertainties about the ways in which microbes and their extracellular enzymes overcome the generally destructive, inhibitory and competitive properties of the soil matrix, and the various strategies they adopt for effective substrate detection and utilization. The complexity of extracellular enzyme activities in depolymerising macromolecular organics is exemplified by lignocellulose degradation and how the many enzymes involved respond to structural diversity and changing nutrient availabilities. The impacts of climate change on microbes and their extracellular enzymes, although of profound importance, are not well understood but we suggest how they may be predicted, assessed and managed. We describe recent advances that allow for the manipulation of extracellular enzyme activities to facilitate bioremediation, carbon sequestration and plant growth promotion. We also contribute to the ongoing debate as to how to assay enzyme activities in soil and what the measurements tell us, in the context of both traditional methods and the newer techniques that are being developed and adopted. Finally, we offer our collective vision of the future of extracellular enzyme research: one that will depend on imaginative thinking as well as technological advances, and be built upon synergies between diverse disciplines.

Soil enzymes in a changing environment: Current knowledge and future directions

In addition to their well-recognized roles in plant nutrition and communities, mycorrhizas can influence the key ecosystem process of soil aggregation. Here we review the contribution of mycorrhizas, mostly focused on arbuscular mycorrhizal fungi (AMF), to soil structure at various hierarchical levels: plant community; individual root; and the soil mycelium. There are a suite of mechanisms by which mycorrhizal fungi can influence soil aggregation at each of these various scales. By extension of these mechanisms to the question of fungal diversity, it is recognized that different species or communities of fungi can promote soil aggregation to different degrees. We argue that soil aggregation should be included in a more complete 'multifunctional' perspective of mycorrhizal ecology, and that in-depth understanding of mycorrhizas/soil process relationships will require analyses emphasizing feedbacks between soil structure and mycorrhizas, rather than a uni-directional approach simply addressing mycorrhizal effects on soils. We finish the discussion by highlighting new tools, developments and foci that will probably be crucial in further understanding mycorrhizal contributions to soil structure.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/j.1469-8137.2006.01750.x

Mycorrhizas and soil structure

A highly controversial issue in global biogeochemistry is the regulation of terrestrial carbon (C) sequestration by soil nitrogen (N) availability. This controversy translates into great uncertainty in predicting future global terrestrial C sequestration. We propose a new framework that centers on the concept of progressive N limitation (PNL) for studying the interactions between C and N in terrestrial ecosystems. In PNL, available soil N becomes increasingly limiting as C and N are sequestered in long-lived plant biomass and soil organic matter. Our analysis focuses on the role of PNL in regulating ecosystem responses to rising atmospheric carbon dioxide concentration, but the concept applies to any perturbation that initially causes C and N to accumulate in organic forms. This article examines conditions under which PNL may or may not constrain net primary production and C sequestration in terrestrial ecosystems. While the PNL-centered framework has the potential to explain diverse experimental...

https://www.jstor.org/stable/10.1641/0006-3568(2004)054%5B0731:PNLOER%5D2.0.CO;2

Progressive Nitrogen Limitation of Ecosystem Responses to Rising Atmospheric Carbon Dioxide

An expectation in soil ecology is that a microbial communities' fungal:bacterial dominance indicates both its response to environmental change and its impact on ecosystem function. We review a selection of the increasing body of literature on this subject and assess the relevance of its expectations by examining the methods used to determine, the impact of environmental factors on, and the expected ecosystem consequences of fungal:bacterial dominance. Considering methods, we observe that fungal:bacterial dominance is contingent on the actual measure used to estimate it. This has not been carefully considered; fungal:bacterial dominance of growth, biomass, and residue indicate different, and not directly relatable aspects, of the microbial community's influence on soil functioning. Considering relationships to environmental factors, we found that shifts in fungal:bacterial dominance were not always in line with the general expectation, in many instances even being opposite to them. This is likely because the traits expected to differentiate bacteria from fungi are often not distinct. Considering the impact of fungal:bacterial dominance on ecosystem function, we similarly found that expectations were not always upheld and this too could be due to trait overlap between these two groups. We explore many of the potential reasons why expectations related to fungal:bacterial dominance were not met, highlighting areas where future research, especially furthering a basic understanding of the ecology of bacteria and fungi, is needed. (C) 2010 Elsevier Ltd. All rights reserved. (Less)

Considering fungal:bacterial dominance in soils – Methods, controls, and ecosystem implications

Nutrient-poor grassland on a silty clay loam overlying calcareous debris was exposed to elevated CO2 for six growing seasons. The CO2 exchange and productivity were persistently increased throughout the experiment, suggesting increases in soil C inputs. At the same time, elevated CO2 lead to increased soil moisture due to reduced evapotransporation. Measurements related to soil microflora did not indicate increased soil C fluxes under elevated CO2. Microbial biomass, soil basal respiration, and the metabolic quotient for CO2 (qCO2) were not altered significantly. PLFA analysis indicated no significant shift in the ratio of fungi to bacteria. 0.5 m KCl extractable organic C and N, indicators of changed DOC and DON concentrations, also remained unaltered. Microbial grazer populations (protozoa, bacterivorous and fungivorous nematodes, acari and collembola) and root feeding nematodes were not affected by elevated CO2. However, total nematode numbers averaged slightly lower under elevated CO2 (−16%, ns) and nematode mass was significantly reduced (−43%, P = 0.06). This reduction reflected a reduction in large-diameter nematodes classified as omnivorous and predacious. Elevated CO2 resulted in a shift towards smaller aggregate sizes at both micro- and macro-aggregate scales; this was caused by higher soil moisture under elevated CO2. Reduced aggregate sizes result in reduced pore neck diameters. Locomotion of large-diameter nematodes depends on the presence of large enough pores; the reduction in aggregate sizes under elevated CO2 may therefore account for the decrease in large nematodes. These animals are relatively high up the soil food web; this decline could therefore trigger top-down effects on the soil food web. The CO2 enrichment also affected the nitrogen cycle. The N stocks in living plants and surface litter increased at elevated CO2, but N in soil organic matter and microbes remained unaltered. Nitrogen mineralization increased markedly, but microbial N did not differ between CO2 treatments, indicating that net N immobilization rates were unaltered. In summary, this study did not provide evidence that soils and soil microbial communities are affected by increased soil C inputs under elevated CO2. On the contrary, available data (13C tracer data, minirhizotron observations, root ingrowth cores) suggests that soil C inputs did not increase substantially. However, we provide first evidence that elevated CO2 can reduce soil aggregation at the scale from µm to mm scale, and that this can affect soil microfaunal populations.

Six years of in situ CO2 enrichment evoke changes in soil structure and soil biota of nutrient‐poor grassland

Elevated concentration of atmospheric carbon dioxide will affect carbon cycling in terrestrial ecosystems. Possible effects include increased carbon input into the soil through the rhizosphere, altered nutrient concentrations of plant litter and altered soil moisture. Consequently, the ongoing rise in atmospheric carbon dioxide might indirectly influence soil biota, decomposition and nutrient transformations.

N-mineralisation and activities of the enzymes invertase, xylanase, urease, protease, arylsulfatase, and alkaline phosphatase were investigated in spring and summer in calcareous grassland, which had been exposed to ambient and elevated CO2 concentrations (365 and 600 μl l−1) for six growing seasons.

In spring, N-mineralisation increased significantly by 30% at elevated CO2, while there was no significant difference between treatments in summer (+3%). The response of soil enzymes to CO2 enrichment was also more pronounced in spring, when alkaline phosphatase and urease activities were increased most strongly by 32 and 21%. In summer, differences of activities between CO2 treatments were greatest in the case of urease and protease (+21 and +17% at elevated CO2).

The stimulation of N-mineralisation and enzyme activities at elevated CO2 was probably caused by higher soil moisture and/or increased root biomass. We conclude that elevated CO2 will enhance below-ground C- and N-cycling in grasslands.

Long term CO2 enrichment stimulates N-mineralisation and enzyme activities in calcareous grassland

Elevated CO2 generally increases plant productivity, and has been found to alter plant community composition in many ecosystems. Because soil microbes depend on plant-derived C and are often associated with specific plant species, elevated CO2 has the potential to alter structure and functioning of soil microbial communities. We investigated soil microbial community structure of a species-rich semi-natural calcareous grassland that had been exposed to elevated CO2 (600 μL L−1) for 6 growing seasons. We analysed microbial community structure using phospholipid fatty acid (PLFA) profiles and DNA fingerprints obtained by Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rDNA fragments amplified by the Polymerase Chain Reaction (PCR). PLFA profiles were not affected by CO2 enrichment and the ratio of fungal and bacterial PLFA did not change. Ordination analysis of DNA fingerprints revealed a significant relation between CO2 enrichment and variation in DNA fingerprints in summer (P=0.01), but not in spring. This variation was due to changes in low-intensity bands, while dominant bands did not differ between CO2 treatments. Diversity of the bacterial community, as assessed by number of bands in DNA fingerprints and calculation of Shannon diversity indices, was not affected by elevated CO2. Overall, only minor effects on microbial community structure were detected, corroborating earlier findings that soil carbon inputs did probably change much less than suggested by plant photosynthetic responses.

Diana Ebersberger

Papers

Six years of in situ CO2 enrichment evoke changes in soil structure and soil biota of nutrient‐poor grassland

Long term CO2 enrichment stimulates N-mineralisation and enzyme activities in calcareous grassland

Effects of long term CO2 enrichment on microbial community structure in calcareous grassland