An integrative approach to understanding microbial diversity: from intracellular mechanisms to community structure

Trade-offs have been put forward as essential to the generation and maintenance of diversity. However, variation in trade-offs is often determined at the molecular level, outside the scope of conventional ecological inquiry. In this study, we propose that understanding the intracellular basis for trade-offs in microbial systems can aid in predicting and interpreting patterns of diversity. First, we show how laboratory experiments and mathematical models have unveiled the hidden intracellular mechanisms underlying trade-offs key to microbial diversity: (i) metabolic and regulatory trade-offs in bacteria and yeast; (ii) life-history trade-offs in bacterial viruses. Next, we examine recent studies of marine microbes that have taken steps toward reconciling the molecular and the ecological views of trade-offs, despite the challenges in doing so in natural settings. Finally, we suggest avenues for research where mathematical modelling, experiments and studies of natural microbial communities provide a unique opportunity to integrate studies of diversity across multiple scales

Soil Phosphate Stable Oxygen Isotopes across Rainfall and Bedrock Gradients

The stable oxygen isotope compositions of soil phosphate (δ¹⁸O_p) were suggested recently to be a tracer of phosphorus cycling in soils and plants. Here we present a survey of bioavailable (resin-extractable or resin-P) inorganic phosphate δ¹⁸O_p across natural and experimental rainfall gradients, and across soil formed on sedimentary and igneous bedrock. In addition, we analyzed the soil HCl-extractable inorganic δ¹⁸O_p, which mainly represents calcium-bound inorganic phosphate. The resin-P values were in the range 14.5–21.2‰. A similar range, 15.6–21.3‰, was found for the HCl-extractable inorganic δ¹⁸O_p, with the exception of samples from a soil of igneous origin that show lower values, 8.2–10.9‰, which indicate that a large fraction of the inorganic phosphate in this soil is still in the form of a primary mineral. The available-P δ¹⁸O_p values are considerably higher than the values we calculated for extracellular hydrolysis of organic phosphate, based on the known fractionation from lab experiments. However, these values are close to the values expected for enzymatic-mediated phosphate equilibration with soil–water. The possible processes that can explain this observation are (1) extracellular equilibration of the inorganic phosphate in the soil; (2) fractionations in the soil are different than the ones measured at the lab; (3) effect of fractionation during uptake; and (4) a flux of intercellular-equilibrated inorganic phosphate from the soil microbiota, which is considerably larger than the flux of hydrolyzed organic-P

The changing carbon cycle at Mauna Loa Observatory

The amplitude of the CO(2) seasonal cycle at the Mauna Loa Observatory (MLO) increased from the early 1970s to the early 1990s but decreased thereafter despite continued warming over northern continents. Because of its location relative to the large-scale atmospheric circulation, the MLO receives mainly Eurasian air masses in the northern hemisphere (NH) winter but relatively more North American air masses in NH summer. Consistent with this seasonal footprint, our findings indicate that the MLO amplitude registers North American net carbon uptake during the warm season and Eurasian net carbon release as well as anomalies in atmospheric circulation during the cold season. From the early 1970s to the early 1990s, our analysis was consistent with that of Keeling et al. [Keeling CD, Chin JFS, Whorf TP (1996) Nature 382:146–149], suggesting that the increase in the MLO CO(2) amplitude is dominated by enhanced photosynthetic drawdown in North America and enhanced respiration in Eurasia. In contrast, the recent decline in the CO(2) amplitude is attributed to reductions in carbon sequestration over North America associated with severe droughts from 1998 to 2003 and changes in atmospheric circulation leading to decreased influence of Eurasian air masses. With the return of rains to the U.S. in 2004, both the normalized difference vegetation index and the MLO amplitude sharply increased, suggesting a return of the North American carbon sink to more normal levels. These findings indicate that atmospheric CO(2) measurements at remote sites can continue to play an important role in documenting changes in land carbon flux, including those related to widespread drought, which may continue to worsen as a result of global warming

Carbon dioxide emitted from live stems of tropical trees is several years old.

Storage carbon (C) pools are often assumed to contribute to respiration and growth when assimilation is insufficient to meet the current C demand. However, little is known of the age of stored C and the degree to which it supports respiration in general. We used bomb radiocarbon ((14)C) measurements to determine the mean age of carbon in CO2 emitted from and within stems of three tropical tree species in Peru. Carbon pools fixed >1 year previously contributed to stem CO2 efflux in all trees investigated, in both dry and wet seasons. The average age, i.e., the time elapsed since original fixation of CO2 from the atmosphere by the plant to its loss from the stem, ranged from 0 to 6 years. The average age of CO2 sampled 5-cm deep within the stems ranged from 2 to 6 years for two of the three species, while CO2 in the stem of the third tree species was fixed from 14 to >20 years previously. Given the consistency of (14)C values observed for individuals within each species, it is unlikely that decomposition is the source of the older CO2. Our results are in accordance with other studies that have demonstrated the contribution of storage reserves to the construction of stem wood and root respiration in temperate and boreal forests. We postulate the high (14)C values observed in stem CO2 efflux and stem-internal CO2 result from respiration of storage C pools within the tree. The observed age differences between emitted and stem-internal CO2 indicate an age gradient for sources of CO2 within the tree: CO2 produced in the outer region of the stem is younger, originating from more recent assimilates, whereas the CO2 found deeper within the stem is older, fueled by several-year-old C pools. The CO2 emitted at the stem-atmosphere interface represents a mixture of young and old CO2. These observations were independent of season, even during a time of severe regional drought. Therefore, we postulate that the use of storage C for respiration occurs on a regular basis challenging the assumption that storage pools serve as substrates for respiration only during times of limited assimilation