Microbes exist in a range of metabolic states (for example, dormant, active and growing) and analysis of ribosomal RNA (rRNA) is frequently employed to identify the 'active' fraction of microbes in environmental samples. While rRNA analyses are no longer commonly used to quantify a population's growth rate in mixed communities, due to rRNA concentration not scaling linearly with growth rate uniformly across taxa, rRNA analyses are still frequently used toward the more conservative goal of identifying populations that are currently active in a mixed community. Yet, evidence indicates that the general use of rRNA as a reliable indicator of metabolic state in microbial assemblages has serious limitations. This report highlights the complex and often contradictory relationships between rRNA, growth and activity. Potential mechanisms for confounding rRNA patterns are discussed, including differences in life histories, life strategies and non-growth activities. Ways in which rRNA data can be used for useful characterization of microbial assemblages are presented, along with questions to be addressed in future studies.

The microbial response to summer desiccation reflects adaptation strategies, setting the stage for a large rainfall-induced soil CO 2 pulse upon rewetting, an important component of the ecosystem carbon budget. In three California annual grasslands, the present (DNA-based) and potentially active (RNA-based) soil bacterial and fungal communities were tracked over a summer season and in response to controlled rewetting of intact soil cores. Phylogenetic marker genes for bacterial (16S) and fungal (28S) RNA and DNA were sequenced, and the abundances of these genes and transcripts were measured. Although bacterial community composition differed among sites, all sites shared a similar response pattern of the present and potentially active bacterial community to dry-down and wet-up. In contrast, the fungal community was not detectably different among sites, and was largely unaffected by dry-down, showing marked resistance to dessication. The potentially active bacterial community changed significantly as summer dry-down progressed, then returned to pre-dry-down composition within several hours of rewetting, displaying spectacular resilience. Upon rewetting, transcript copies of bacterial rpoB genes increased consistently, reflecting rapid activity resumption. Acidobacteria and Actinobacteria were the most abundant phyla present and potentially active, and showed the largest changes in relative abundance. The relative increase (Actinobacteria) and decrease (Acidobacteria) with dry-down, and the reverse responses to rewetting reflected a differential response, which was conserved at the phylum level and consistent across sites. These contrasting desiccation-related bacterial life-strategies suggest that predicted changes in precipitation patterns may affect soil nutrient and carbon cycling by differentially impacting activity patterns of microbial communities.

In the past two decades, a large number of studies have investigated the relationship between biodiversity and ecosystem functioning, most of which focussed on a limited set of ecosystem variables. The Jena Experiment was set up in 2002 to investigate the effects of plant diversity on element cycling and trophic interactions, using a multi-disciplinary approach. Here, we review the results of 15 years of research in the Jena Experiment, focussing on the effects of manipulating plant species richness and plant functional richness. With more than 85,000 measures taken from the plant diversity plots, the Jena Experiment has allowed answering fundamental questions important for functional biodiversity research. First, the question was how general the effect of plant species richness is, regarding the many different processes that take place in an ecosystem. About 45% of different types of ecosystem processes measured in the ‘main experiment’, where plant species richness ranged from 1 to 60 species, were significantly affected by plant species richness, providing strong support for the view that biodiversity is a significant driver of ecosystem functioning. Many measures were not saturating at the 60-species level, but increased linearly with the logarithm of species richness. There was, however, great variability in the strength of response among different processes. One striking pattern was that many processes, in particular belowground processes, took several years to respond to the manipulation of plant species richness, showing that biodiversity experiments have to be long-term, to distinguish trends from transitory patterns. In addition, the results from the Jena Experiment provide further evidence that diversity begets stability, for example stability against invasion of plant species, but unexpectedly some results also suggested the opposite, e.g. when plant communities experience severe perturbations or elevated resource availability. This highlights the need to revisit diversity–stability theory. Second, we explored whether individual plant species or individual plant functional groups, or biodiversity itself is more important for ecosystem functioning, in particular biomass production. We found strong effects of individual species and plant functional groups on biomass production, yet these effects mostly occurred in addition to, but not instead of, effects of plant species richness. Third, the Jena Experiment assessed the effect of diversity on multitrophic interactions. The diversity of most organisms responded positively to increases in plant species richness, and the effect was stronger for above- than for belowground organisms, and stronger for herbivores than for carnivores or detritivores. Thus, diversity begets diversity. In addition, the effect on organismic diversity was stronger than the effect on species abundances. Fourth, the Jena Experiment aimed to assess the effect of diversity on N, P and C cycling and the water balance of the plots, separating between element input into the ecosystem, el...

[1] We reviewed responses of nitrification, denitrification, and soil N 2 O efflux to elevated CO 2 , N availability, and temperature, based on published experimental results. We used meta-analysis to estimate the magnitude of response of soil N 2 O emissions, nitrifying enzyme activity (NEA), denitrifying enzyme activity (DEA), and net and gross nitrification across experiments. We found no significant overall effect of elevated CO 2 on N 2 O fluxes. DEA and NEA significantly decreased at elevated CO 2 ; however, gross nitrification was not modified by elevated CO 2 , and net nitrification increased. The negative overall response of DEA to elevated CO 2 was associated with decreased soil [NO 3 À ], suggesting that reduced availability of electron acceptors may dominate the responses of denitrification to elevated CO 2 . N addition significantly increased field and laboratory N 2 O emissions, together with gross and net nitrification, but the effect of N addition on field N 2 O efflux was not correlated to the amount of N added. The effects of elevated temperature on DEA, NEA, and net nitrification were not significant: The small number of studies available stress the need for more warming experiments in the field. While N addition had large effects on measurements of nitrification and denitrification, the effects of elevated CO 2 were less pronounced and more variable, suggesting that increased N deposition is likely to affect belowground N cycling with a magnitude of change that is much larger than that caused by elevated CO 2 .

Summary Recent studies have highlighted a direct, fast transfer of recently assimilated C from the tree canopy to the soil. However, the effect of environmental changes on this flux remains largely unknown. We investigated the effects of drought on the translocation of recently assimilated C, by pulse‐labelling 1.5‐yr‐old beech tree mesocosms with 13CO2. 13C signatures were then measured daily for 1 wk in leaves, twigs, coarse and fine root water‐soluble and total organic matter, phloem organic matter, soil microbial biomass and soil CO2 efflux. Drought reduced C assimilation and doubled the residence time of recently assimilated C in leaf biomass. In phloem organic matter, the 13C label peaked immediately after labelling then decayed exponentially in the control treatment, while under drought it peaked 4 d after labelling. In soil microbial biomass, the label peaked 1 d after labelling in the control treatment, whereas under drought no peak was measured. Two days after labelling, drought decreased the contribution of recently assimilated C to soil CO2 efflux by 33%. Our study showed that drought reduced the coupling between canopy photosynthesis and belowground processes. This will probably affect soil biogeochemical cycling, with potential consequences including slower soil nitrogen cycling and changes in C‐sequestration potential under future climate conditions.

The (13)C isotopic signature (C stable isotope ratio; delta(13)C) of CO(2) respired from forest ecosystems and their particular compartments are known to be influenced by temporal changes in environmental conditions affecting C isotope fractionation during photosynthesis. Whereas most studies have assessed temporal variation in delta(13)C of ecosystem-respired CO(2) on a day-to-day scale, not much information is available on its diel dynamics. We investigated environmental and physiological controls over potential temporal changes in delta(13)C of respired CO(2) by following the short-term dynamics of the (13)C signature from newly assimilated organic matter pools in the needles, via phloem-transported organic matter in twigs and trunks, to trunk-, soil- and ecosystem-respired CO(2). We found a strong 24-h periodicity in delta(13)C of organic matter in leaf and twig phloem sap, which was strongly dampened as carbohydrates were transported down the trunk. Periodicity reappeared in the delta(13)C of trunk-respired CO(2), which seemed to originate from apparent respiratory fractionation rather than from changes in delta(13)C of the organic substrate. The diel patterns of delta(13)C in soil-respired CO(2) are partly explained by soil temperature and moisture and are probably due to changes in the relative contribution of heterotrophic and autotrophic CO(2) fluxes to total soil efflux in response to environmental conditions. Our study shows that direct relations between delta(13)C of recent assimilates and respired CO(2) may not be present on a diel time scale, and other factors lead to short-term variations in delta(13)C of ecosystem-emitted CO(2). On the one hand, these variations complicate ecosystem CO(2) flux partitioning, but on the other hand they provide new insights into metabolic processes underlying respiratory CO(2) emission.

The analysis of d 13 C and d 18 O in tree-ring archives offers retrospective insights into environmental conditions and ecophysiological processes. While photosynthetic carbon isotope discrimination and evaporative oxygen isotope enrichment are well understood, we lack information on how the isotope signal is altered by downstream metabolic processes.In Pinus sylvestris, we traced the isotopic signals from their origin in the leaf water (d 18 O) or the newly assimilated carbon (d 13 C), via phloem sugars to the tree-ring, over a time-scale that ranges from hours to a growing season.Seasonally, variable 13 C enrichment of sugars related to phloem loading and transport did lead to uncoupling between d 13 C in the tree-ring, and the ci/ca ratio at the leaf level. In contrast, the oxygen isotope signal was transferred from the leaf water to the tree-ring with an expected enrichment of 27‰, with time-lags of approximately 2 weeks and with a 40% exchange between organic oxygen and xylem water oxygen during cellulose synthesis.This integrated overview of the fate of carbon and oxygen isotope signals within the model tree species P. sylvestris provides a novel physiological basis for the interpretation of d 13 C and d 18 O in tree-ring ecology.

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