Soil microbial moisture dependences and responses to drying–rewetting: The legacy of 18 years drought

Climate change will alter precipitation patterns with consequences for soil C cycling. An understanding of how fluctuating soil moisture affects microbial processes is therefore critical to predict responses to future global change. We investigated how long‐term experimental field drought influences microbial tolerance to lower moisture levels (“resistance”) and ability to recover when rewetted after drought (“resilience”), using soils from a heathland which had been subjected to experimental precipitation reduction during the summer for 18 years. We tested whether drought could induce increased resistance, resilience, and changes in the balance between respiration and bacterial growth during perturbation events, by following a two‐tiered approach. We first evaluated the effects of the long‐term summer drought on microbial community functioning to drought and drying–rewetting (D/RW), and second tested the ability to alter resistance and resilience through additional perturbation cycles. A history of summer drought in the field selected for increased resilience but not resistance, suggesting that rewetting after drought, rather than low moisture levels during drought, was the selective pressure shaping the microbial community functions. Laboratory D/RW cycles also selected for communities with a higher resilience rather than increased resistance. The ratio of respiration to bacterial growth during D/RW perturbation was lower for the field drought‐exposed communities and decreased for both field treatments during the D/RW cycles. This suggests that cycles of D/RW also structure microbial communities to respond quickly and efficiently to rewetting after drought. Our findings imply that microbial communities can adapt to changing climatic conditions and that this might slow the rate of soil C loss predicted to be induced by future cyclic drought.     

Parkin reverses TDP‐43‐induced cell death and failure of amino acid homeostasis

The E3 ubiquitin ligase Parkin plays a central role in the pathogenesis of many neurodegenerative diseases. Parkin promotes specific ubiquitination and affects the localization of transactivation response DNA‐binding protein 43 (TDP‐43), which controls the translation of thousands of mRNAs. Here we tested the effects of lentiviral Parkin and TDP‐43 expression on amino acid metabolism in the rat motor cortex using high frequency ¹³C NMR spectroscopy. TDP‐43 expression increased glutamate levels, decreased the levels of other amino acids, including glutamine, aspartate, leucine and isoleucine, and impaired mitochondrial tricarboxylic acid cycle. TDP‐43 induced lactate accumulation and altered the balance between excitatory (glutamate) and inhibitory (GABA) neurotransmitters. Parkin restored amino acid levels, neurotransmitter balance and tricarboxylic acid cycle metabolism, rescuing neurons from TDP‐43‐induced apoptotic death. Furthermore, TDP‐43 expression led to an increase in 4E‐BP levels, perhaps altering translational control and deregulating amino acid synthesis; while Parkin reversed the effects of TDP‐43 on the 4E‐BP signaling pathway. Taken together, these data suggest that Parkin may affect TDP‐43 localization and mitigate its effects on 4E‐BP signaling and loss of amino acid homeostasis.

     

Deer do not affect short‐term rates of vegetation recovery in overwash fans on Fire Island after Hurricane Sandy

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Carbon sequestration in soil in a semi‐natural Miscanthus sinensis grassland and Cryptomeria japonica forest plantation in Aso,Kumamoto, Japan

Although Miscanthus sinensis grasslands (Misc‐GL) and Cryptomeria japonica forest plantations (Cryp‐FP) are proposed bioenergy feedstock systems, their relative capacity to sequester C may be an important factor in determining their potential for sustainable bioenergy production. Therefore, our objective was to quantify changes in soil C sequestration 47 years after a Misc‐GL was converted to a Cryp‐FP. The study was conducted on adjacent Misc‐GL and Cryp‐FP located on Mt. Aso, Kumamoto, Japan. After Cryp‐FP establishment, only the Misc‐GL continued to be managed by annual burning every March. Mass C and N, δ¹³C, and δ¹⁵N at 0–30 cm depth were measured in 5 cm increments. Carbon and N concentrations, C:N ratio, δ¹³C, and δ¹⁵N were measured in litter and/or ash, and rhizomes or roots. Although C input in Misc‐GL by M. sinensis was approximately 36% of that in Cryp‐FP by C. japonica, mean annual soil C sequestration in Misc‐GL (503 kg C ha^?1 yr^?1) was higher than that in Cryp‐FP (284 kg C ha^?1 yr^?1). This was likely the result of larger C input from aboveground litter to soil, C‐quality (C:N ratio and lignin concentration in aboveground litter) and possibly more recalcitrant C (charcoal) inputs by annual burning. The difference in soil δ¹⁵N between sites indicated that organic C with N had greater cycling between heterotrophic microbes and soil and produces more recalcitrant humus in Misc‐GL than in Cryp‐FP. Our data indicate that in terms of soil C sequestration, maintenance of Misc‐GL may be more advantageous than conversion to Cryp‐FP in Aso, Japan.     

Influence of short‐term drought conditions and subsequent re‐watering on the physiology and proteome of Lolium multiflorum/Festuca arundinacea introgression forms,with contrasting levels of tolerance to long‐term drought

Festuca arundinacea is a drought tolerant species. Lolium multiflorum has better forage quality but lower tolerance to abiotic stresses. Their hybrids offer an opportunity to perform research on the molecular basis of tolerance to drought. The aim of this work was to recognise the mechanisms of response to short‐term drought (11 days) in a glasshouse in two L. multiflorum/F. arundinacea introgression forms with distinct levels of tolerance to long‐term drought (14 weeks) in the field. Measurements of physiological parameters, analyses of protein accumulation profiles using two‐dimensional gel electrophoresis, and mass spectrometry identification of proteins, which were accumulated differentially between the selected genotypes during short‐term drought, were performed. Genotype 7/6, with lower yield potential during 14 weeks of drought, and lower ability to re‐grow after watering, had a higher capacity for photosynthesis during 11 days of drought. Genotype 4/10, more tolerant to long‐term drought, was able to repair damaged cell membranes after watering and was also characterised by lower transpiration during short‐term drought. A total of 455 proteins were analysed, and the 17 that were differentially accumulated between the two genotypes were identified. The results of physiological and proteomic research led to a hypothesis that the higher photosynthetic capacity of genotype 7/6 could be due to a more efficient Calvin cycle, supported by higher accumulation of crucial proteins involving chloroplast aldolase.     

Temperature sensitivity of biomass‐specific microbial exo‐enzyme activities and CO2 efflux is resistant to change across short‐ and long‐term timescales

Accurate representation of temperature sensitivity (Q₁₀) of soil microbial activity across time is critical for projecting soil CO₂ efflux. As microorganisms mediate soil carbon (C) loss via exo‐enzyme activity and respiration, we explore temperature sensitivities of microbial exo‐enzyme activity and respiratory CO₂ loss across time and assess mechanisms associated with these potential changes in microbial temperature responses. We collected soils along a latitudinal boreal forest transect with different temperature regimes (long‐term timescale) and exposed these soils to laboratory temperature manipulations at 5, 15, and 25°C for 84 days (short‐term timescale). We quantified temperature sensitivity of microbial activity per g soil and per g microbial biomass at days 9, 34, 55, and 84, and determined bacterial and fungal community structure before the incubation and at days 9 and 84. All biomass‐specific rates exhibited temperature sensitivities resistant to change across short‐ and long‐term timescales (mean Q₁₀ = 2.77 ± 0.25, 2.63 ± 0.26, 1.78 ± 0.26, 2.27 ± 0.25, 3.28 ± 0.44, 2.89 ± 0.55 for β‐glucosidase, N‐acetyl‐β‐d ‐glucosaminidase, leucine amino peptidase, acid phosphatase, cellobiohydrolase, and CO₂ efflux, respectively). In contrast, temperature sensitivity of soil mass‐specific rates exhibited either resilience (the Q₁₀ value changed and returned to the original value over time) or resistance to change. Regardless of the microbial flux responses, bacterial and fungal community structure was susceptible to change with temperature, significantly differing with short‐ and long‐term exposure to different temperature regimes. Our results highlight that temperature responses of microbial resource allocation to exo‐enzyme production and associated respiratory CO₂ loss per unit biomass can remain invariant across time, and thus, that vulnerability of soil organic C stocks to rising temperatures may persist in the long term. Furthermore, resistant temperature sensitivities of biomass‐specific rates in spite of different community structures imply decoupling of community constituents and the temperature responses of soil microbial activities.     

The combined effects of a long‐term experimental drought and an extreme drought on the use of plant‐water sources in a Mediterranean forest

Vegetation in water‐limited ecosystems relies strongly on access to deep water reserves to withstand dry periods. Most of these ecosystems have shallow soils over deep groundwater reserves. Understanding the functioning and functional plasticity of species‐specific root systems and the patterns of or differences in the use of water sources under more frequent or intense droughts is therefore necessary to properly predict the responses of seasonally dry ecosystems to future climate. We used stable isotopes to investigate the seasonal patterns of water uptake by a sclerophyll forest on sloped terrain with shallow soils. We assessed the effect of a long‐term experimental drought (12 years) and the added impact of an extreme natural drought that produced widespread tree mortality and crown defoliation. The dominant species, Quercus ilex, Arbutus unedo and Phillyrea latifolia, all have dimorphic root systems enabling them to access different water sources in space and time. The plants extracted water mainly from the soil in the cold and wet seasons but increased their use of groundwater during the summer drought. Interestingly, the plants subjected to the long‐term experimental drought shifted water uptake toward deeper (10–35 cm) soil layers during the wet season and reduced groundwater uptake in summer, indicating plasticity in the functional distribution of fine roots that dampened the effect of our experimental drought over the long term. An extreme drought in 2011, however, further reduced the contribution of deep soil layers and groundwater to transpiration, which resulted in greater crown defoliation in the drought‐affected plants. This study suggests that extreme droughts aggravate moderate but persistent drier conditions (simulated by our manipulation) and may lead to the depletion of water from groundwater reservoirs and weathered bedrock, threatening the preservation of these Mediterranean ecosystems in their current structures and compositions.     

Stable isotope composition and parasitic infections of harbor seal young‐of‐the‐year used as prey‐based diet indicators

The stable isotope composition (δ¹³C and δ¹⁵N values) of harbor seals (Phoca vitulina) is influenced by their diet. Young‐of‐the‐year during lactation and postweaning fast are expected be enriched in ¹⁵N compared to foraging seals. We studied the temporal variation of stable isotope composition of young‐of‐the‐year and adults to determine from which point in time the young‐of‐the‐year tissues (i.e., muscles and vibrissae) are influenced by independent foraging only. These results were compared with the development of trophically transmitted parasitic infections. The δ¹⁵N values in young‐of‐the‐year muscles decreased from June (20.3‰ ± 0.5‰) to October (18.5‰ ± 0.4‰), while those of foraging seals were all year long below 19.2‰. This decrease coincides with the increase of parasitic infections in young‐of‐the‐year, reflecting a shift to fish diet. Together these results suggest that the muscles of the young‐of‐the‐year older than 5–6 mo reflect independent foraging and that they can therefore be used in community diet studies. The nursing signal in vibrissae was unclear, as the δ¹⁵N values of young‐of‐the‐year were stable over time, whereas those of adults varied seasonally. However, δ¹⁵N values of nursing pups were significantly higher than those of adults in May and June, maybe due to their reliance on milk.     

Landscape heterogeneity shapes host‐parasite interactions and results in apparent plant–virus codivergence

Knowledge on how landscape heterogeneity shapes host–parasite interactions is central to understand the emergence, dynamics and evolution of infectious diseases. However, this is an underexplored subject, particularly for plant–virus systems. Here, we analyse how landscape heterogeneity influences the prevalence, spatial genetic structure, and temporal dynamics of Pepper golden mosaic and Pepper huasteco yellow vein begomoviruses infecting populations of the wild pepper Capsicum annuum glabriusculum (chiltepin) in Mexico. Environmental heterogeneity occurred at different nested spatial scales (host populations within biogeographical provinces), with levels of human management varying among host population within a province. Results indicate that landscape heterogeneity affects the epidemiology and genetic structure of chiltepin‐infecting begomoviruses in a scale‐specific manner, probably related to conditions favouring the viruses' whitefly vector and its dispersion. Increased levels of human management of the host populations were associated with higher virus prevalence and erased the spatial genetic structure of the virus populations. Also, environmental heterogeneity similarly shaped the spatial genetic structures of host and viruses. This resulted in the congruence between host and virus phylogenies, which does not seem to be due to host‐virus co‐evolution. Thus, results provide evidence of the key role of landscape heterogeneity in determining plant–virus interactions.     

Phylogenetic conservatism in plant‐soil feedback and its implications for plant abundance

We examined whether plant‐soil feedback and plant‐field abundance were phylogenetically conserved. For 57 co‐occurring native and exotic plant species from an old field in Canada, we collected a data set on the effects of three soil biota treatments on plant growth: net whole‐soil feedback (combined effects of mutualists and antagonists), feedback with arbuscular mycorrhizal fungi (AMF) collected from soils of conspecific plants, and feedback with Glomus etunicatum, a dominant mycorrhizal fungus. We found phylogenetic signal in both net whole‐soil feedback and feedback with AMF of conspecifics; conservatism was especially strong among native plants but absent among exotics. The abundance of plants in the field was also conserved, a pattern underlain by shared plant responses to soil biota. We conclude that soil biota influence the abundance of close plant relatives in nature.     

Ecosystem development in short‐term postglacial chronosequences: N and P limitation in glacier forelands from Santa Inés Island,Magellan Strait

Glacier foreland moraines provide an ideal model to examine the patterns of ecosystem development and the evolution of nitrogen and phosphorous limitation over successional time. In this paper, we focus on a 400‐year soil chronosequence in the glacier forelands of Santa Inés Island in the Magellan Strait, southern Chile by examining forest development on phosphorus (P)‐poor substrates in a uniquely unpolluted region of the world. Results show a steady increase in tree basal area and a humped trend in tree species richness over four centuries of stand development. The increase in basal area suggests that the late successional tree species were more efficient nutrient users than earlier successional ones. Total contents of carbon (C) and nitrogen (N) in soils increased during the chronosequence, reaching an asymptote in late succession. The net increases in soil C : N, C : P and N : P ratios observed over successional time suggest that nutrient limitation is maximal in 400‐year‐old substrates. Foliar C : N and C : P ratios also increased over time to reach an asymptote in old‐growth stages, following soil stoichiometric relationships; however the foliar N‐to‐P ratio remained constant throughout the chronosequence. Biological N fixation was greater in early postglacial succession, associated with the presence of the symbiotic N‐fixer Gunnera magellanica. Declining trends of δ¹⁵N in surface soils through the 400‐year chronosequence are evidence of decreasing N losses in old‐growth forests. In synthesis, glacier foreland chronosequences at this high South American latitude provide evidence for increasing efficiency of N and P use in the ecosystem, with the replacement of shade‐intolerant pioneers by more efficient, shade‐tolerant tree species. This pattern of ecosystem development produces a constant foliar N : P ratio, regardless of variation in soil N‐to‐P ratio over four centuries.     

Plant‐facilitated effects of exotic earthworm Pontoscolex corethrurus on the soil carbon and nitrogen dynamics and soil microbial community in a subtropical field ecosystem

Earthworms and plants greatly affect belowground properties; however, their combined effects are more attractive based on the ecosystem scale in the field condition. To address this point, we manipulated earthworms (exotic endogeic species Pontoscolex corethrurus) and plants (living plants [native tree species Evodia lepta] and artificial plants) to investigate their combined effects on soil microorganisms, soil nutrients, and soil respiration in a subtropical forest. The manipulation of artificial plants aimed to simulate the physical effects of plants (e.g., shading and interception of water) such that the biological effects of plants could be evaluated separately. We found that relative to the controls, living plants but not artificial plants significantly increased the ratio of fungal to bacterial phospholipid fatty acids (PLFAs) and fungal PLFAs. Furthermore, earthworms plus living plants significantly increased the soil respiration and decreased the soil NH₄⁺‐N, which indicates that the earthworm effects on the associated carbon, and nitrogen processes were greatly affected by living plants. The permutational multivariate analysis of variance results also indicated that living plants but not earthworms or artificial plants significantly changed the soil microbial community. Our results suggest that the effects of plants on soil microbes and associated soil properties in this study were largely explained by their biological rather than their physical effects.     

Tracking C and N dynamics and stabilization in soil amended with wheat residue and its corresponding bioethanol by‐product: a 13C/15N study

Removing agricultural cellulosic residues from fields for the production of ‘second generation biofuels'has the potential to profoundly alter C and N cycling in soil, increasing the risk of soil organic matter depletion and favoring soil–atmosphere gaseous exchanges. However, these negative impacts could potentially be offset by amending the soil with the solid by‐product which is generated during bioethanol production. In a 100 days laboratory study, we investigated the fate of C and N after soil amendment with doubly labeled (¹³C, ¹⁵N) wheat residue (WR) and the corresponding bioethanol by‐product (i.e. nonfermentable wheat residue NFWR) with and without extra N addition. Substituting WR with the corresponding amount of recovered bioethanol by‐product partially compensated the C losses of full crop residue removal. When the equivalent amount of C was added as WR and NFWR, NFWR‐derived C was found in significantly higher proportion in macroaggregates in soil (17.0 vs. 8.9%) after 100 days. Addition of both WR and NFWR reduced soil organic C (SOC) mineralization, i.e. it caused a negative priming effect in soil. However, this pattern was reversed when extra N was added. Both WR and NFWR increased the proportion of soil water‐stable macroaggregates from 16% (in control) to 20–24% (in the different treatments). The results suggest that the more recalcitrant compounds derived from bioethanol production may stabilize more strongly and persist within the protected fractions of SOM pools. Our study demonstrates that NFWR, compared with WR application, neither increased N₂O emissions nor had a negative impact on aggregate formation in the midterm. This demonstrates that NFWR has potential for replenishing SOC stocks.     

Marine moult migration of the freshwater Scaly‐sided Merganser Mergus squamatus revealed by stable isotopes and geolocators

Scaly‐sided Mergansers Mergus squamatus breed on freshwater rivers in far eastern Russia, Korea and China, wintering in similar habitats in China and Korea, but nothing was known of their moulting habitat. To investigate the moult strategies of this species, we combined wing feather stable isotope ratios (males and females) with geolocator data (nesting females) to establish major habitat types (freshwater, brackish or saltwater) used by both sexes during wing moult. Although most Scaly‐sided Mergansers of both sexes probably moult on freshwater, some males and non‐breeding and failed breeding females appeared to undertake moult migration to brackish and marine waters. Given the previous lack of any surveys of coastal or estuarine waters for this species during the moult period, these findings suggest important survey needs for the effective conservation of the species during the flightless moult period.     

Impacts of 3 years of elevated atmospheric CO2 on rhizosphere carbon flow and microbial community dynamics

Carbon (C) uptake by terrestrial ecosystems represents an important option for partially mitigating anthropogenic CO₂ emissions. Short‐term atmospheric elevated CO₂ exposure has been shown to create major shifts in C flow routes and diversity of the active soil‐borne microbial community. Long‐term increases in CO₂ have been hypothesized to have subtle effects due to the potential adaptation of soil microorganism to the increased flow of organic C. Here, we studied the effects of prolonged elevated atmospheric CO₂ exposure on microbial C flow and microbial communities in the rhizosphere. Carex arenaria (a nonmycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown at defined atmospheric conditions differing in CO₂ concentration (350 and 700 ppm) for 3 years. During this period, C flow was assessed repeatedly (after 6 months, 1, 2, and 3 years) by ¹³C pulse‐chase experiments, and label was tracked through the rhizosphere bacterial, general fungal, and arbuscular mycorrhizal fungal (AMF) communities. Fatty acid biomarker analyses and RNA‐stable isotope probing (RNA‐SIP), in combination with real‐time PCR and PCR‐DGGE, were used to examine microbial community dynamics and abundance. Throughout the experiment the influence of elevated CO₂ was highly plant dependent, with the mycorrhizal plant exerting a greater influence on both bacterial and fungal communities. Biomarker data confirmed that rhizodeposited C was first processed by AMF and subsequently transferred to bacterial and fungal communities in the rhizosphere soil. Over the course of 3 years, elevated CO₂ caused a continuous increase in the ¹³C enrichment retained in AMF and an increasing delay in the transfer of C to the bacterial community. These results show that, not only do elevated atmospheric CO₂ conditions induce changes in rhizosphere C flow and dynamics but also continue to develop over multiple seasons, thereby affecting terrestrial ecosystems C utilization processes.     

Soil carbon stocks and carbon sequestration rates in seminatural grassland in Aso region,Kumamoto, Southern Japan

Global soil carbon (C) stocks account for approximately three times that found in the atmosphere. In the Aso mountain region of Southern Japan, seminatural grasslands have been maintained by annual harvests and/or burning for more than 1000 years. Quantification of soil C stocks and C sequestration rates in Aso mountain ecosystem is needed to make well‐informed, land‐use decisions to maximize C sinks while minimizing C emissions. Soil cores were collected from six sites within 200 km² (767–937 m asl.) from the surface down to the k‐Ah layer established 7300 years ago by a volcanic eruption. The biological sources of the C stored in the Aso mountain ecosystem were investigated by combining C content at a number of sampling depths with age (using ¹⁴C dating) and δ¹³C isotopic fractionation. Quantification of plant phytoliths at several depths was used to make basic reconstructions of past vegetation and was linked with C‐sequestration rates. The mean total C stock of all six sites was 232 Mg C ha^?1 (28–417 Mg C ha^?1), which equates to a soil C sequestration rate of 32 kg C ha^?1 yr^?1 over 7300 years. Mean soil C sequestration rates over 34, 50 and 100 years were estimated by an equation regressing soil C sequestration rate against soil C accumulation interval, which was modeled to be 618, 483 and 332 kg C ha^?1 yr^?1, respectively. Such data allows for a deeper understanding in how much C could be sequestered in Miscanthus grasslands at different time scales. In Aso, tribe Andropogoneae (especially Miscanthus and Schizoachyrium genera) and tribe Paniceae contributed between 64% and 100% of soil C based on δ¹³C abundance. We conclude that the seminatural, C₄‐dominated grassland system serves as an important C sink, and worthy of future conservation.     

Evidence for species‐specific plant responses to soil microbial communities from remnant and degraded land provides promise for restoration

Below‐ground interactions between soil microbial communities and plants play important roles in shaping plant community structure, but are currently poorly understood. Understanding these processes has important practical implications, including for restoration. In this study, we investigated whether soil microbes from remnant areas can aid the restoration of old‐fields, and whether soil microbes from an old‐field encourages further invasive establishment. In a glasshouse experiment, we measured growth and survival of two native grasses (Austrostipa nodosa and Rytidosperma auriculatum) and an invasive grass (Lolium rigidum) grown in sterile soil inoculated with whole soil from three locations: an old‐field, a remnant grassland, and a seed orchard planted with native grasses 7 years ago. Plants grown in sterile, non‐inoculated soil acted as controls. The orchard inoculant was included to test whether soil microbes from an area cultivated with native grasses induced plant responses similar to remnant areas. The remnant treatment resulted in the highest biomass and no mortality for R. auriculatum. All inoculant types increased the biomass of the invasive species equally. The native grass, A. nodosa, was the most sensitive to the addition of inoculum, whereas the invasive L. rigidum suffered very low mortality across all treatments. Overall, mortality was highest in the old‐field treatment at 42.9%. These results give insights into how soil microbes can affect community structure and dynamics, e.g. the high mortality of natives with old‐field inoculant may be one mechanism that allows invasive species to dominate. Poorer performance of native species with the orchard inoculant suggests it would not make a suitable replacement for remnant soil; therefore, more work is needed to understand the requirements of target species and their interactions before this technique can be exploited to maximum benefit.