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Freeze–thaw (FT) events exert a great physiological stress on the soil microbial community and thus significantly impact soil biogeochemical processes. Studies often show ambiguous and contradicting results, because a multitude of environmental factors affect biogeochemical responses to FT. Thus, a better understanding of the factors driving and regulating microbial responses to FT events is required. Soil chronosequences allow more focused comparisons among soils with initially similar start conditions. We therefore exposed four soils with contrasting organic carbon contents and opposing soil age (i.e., years after restoration) from a postmining agricultural chronosequence to three consecutive FT events and evaluated soil biochgeoemical responses after thawing. The major microbial biomass carbon losses occurred after the first FT event, while microbial biomass N decreased more steadily with subsequent FT cycles. This led to an immediate and lasting decoupling of microbial biomass carbon:nitrogen stoichiometry. After the first FT event, basal respiration and the metabolic quotient (i.e., respiration per microbial biomass unit) were above pre-freezing values and thereafter decreased with subsequent FT cycles, demonstrating initially high dissimilatory carbon losses and less and less microbial metabolic activity with each iterative FT cycle. As a consequence, dissolved organic carbon and total dissolved nitrogen increased in soil solution after the first FT event, while a substantial part of the liberated nitrogen was likely lost through gaseous emissions. Overall, high-carbon soils were more vulnerable to microbial biomass losses than low-carbon soils. Surprisingly, soil age explained more variation in soil chemical and microbial responses than soil organic carbon content. Further studies are needed to dissect the factors associated with soil age and its influence on soil biochemical responses to FT events. [ABSTRACT FROM AUTHOR]

Oomycetes are a ubiquitous protistan lineage including devastating crop parasites. Although their ecology in agrosystems has been widely studied, little is known of their distribution in natural and semi-natural ecosystems and how they respond to edaphic and environmental factors. We provide here a baseline of the diversity and distribution of soil oomycetes, classified by lifestyles (biotrophy, hemibiotrophy and saprotrophy), at the landscape scale in temperate grassland and forest. From 600 soil samples, we obtained 1148 operational taxonomy units representing ~ 20 million Illumina reads (region V4, 18S rRNA gene). We found a majority of hemibiotrophic plant pathogens, which are parasites spending part of their life cycle as saprotrophs after the death of the host. Overall both grassland and forest constitute an important reservoir of plant pathogens. Distance-based RDA models identified soil type and mineral soil C/N ratio as the most influential factors in shaping oomycete communities in grassland and forest. Edaphic conditions and human-induced management intensification in forest triggered opposite responses in the relative abundances of obligate biotrophs and hemibiotrophs, suggesting different ecological requirements of these two lifestyles. [ABSTRACT FROM AUTHOR]

Two greenhouse experiments using soils from long-term field plots were carried out to test whether and how soil factors modulated by organic amendments feed back to rice plant growth and defense against an aboveground herbivore, the planthopper Nilaparvata lugens. Using factorial combinations of sterilized soil and soil inocula obtained from chemically amended plots (i.e., control treatment) or chemically plus organically amended plots (i.e., organic treatment), we disentangled the effects of biotic and abiotic soil properties on plant and planthopper performance. We found that, compared with abiotic soil properties, soil biological factors were the main drivers in regulating plant growth performance. Specifically, soil biota that are shaped by the organic treatment had high microbial abundance and diversity and enhanced rice plant tolerance (i.e., increasing plant total biomass) and resistance (i.e., decreasing amino acid and sugar concentrations) to planthoppers. Moreover, the organic treatment simultaneously increased plant growth and defense against planthoppers, which could be explained by high soil nutrient availability driven by soil biota. Our results demonstrate the importance of synergistic effects of soil biota and soil abiotic factors on plant growth and resistance to herbivory. These findings are important for better understanding the mechanisms and impacts of ecological intensification as well as the potential of steering soil communities to reduce the use of chemical fertilizers and pesticides and further optimize crop production. [ABSTRACT FROM AUTHOR]

A new species of coprophagous scarabaeid, Synapsis puluongensis sp. nov., is described based on six specimens collected in Pu Luong Nature Reserve in central Vietnam. The new species can be clearly distinguished from the remaining species of Synapsis Bates, 1868 by the following characters: hypomeral cavities present but not covered by red macrosetae; mesepisternal cavities absent; elytral striae extremely strong, bearing close and strong punctures; metafemora with dense and strong punctures in ventral view. Redescription of S. horaki Zídek & Pokorný, 2010 based on new material is also presented. Key to species of the genus Synapsis from Vietnam is provided. [ABSTRACT FROM AUTHOR]

A new species of coprophagous scarabaeid, Synapsis puluongensis sp. nov., is described based on six specimens collected in Pu Luong Nature Reserve in central Vietnam. The new species can be clearly distinguished from the remaining species of Synapsis Bates, 1868 by the following characters: hypomeral cavities present but not covered by red macrosetae; mesepisternal cavities absent; elytral striae extremely strong, bearing close and strong punctures; metafemora with dense and strong punctures in ventral view. Redescription of S. horaki Zídek & Pokorný, 2010 based on new material is also presented. Key to species of the genus Synapsis from Vietnam is provided. [ABSTRACT FROM AUTHOR]

Abstract: The genus Diaphoropodon, Archer 1869, comprises filose amoebae with agglutinated tests made of quartz grains, diatom frustules and other particulate materials. The key trait of the genus is a hyaline theca covered with numerous 5‐ to 10‐μm‐long, hairlike rods. Based on SSU rDNA phylogeny, we show that Diaphoropodon groups closely to Lecythium, a testate amoeba genus with a flexible but naked theca. Electron microscopic images reveal that the rods of Diaphoropodon are not perforating the test but lie randomly distributed on the surface of the amoeba. Comparing fairly naked cells from our cultures with cells from the environment leads to the conclusion that these rods play a role in agglutinating the material on the test. [ABSTRACT FROM AUTHOR]

DNA repair is essential for life, yet its efficiency declines with age for reasons that are unclear. Numerous proteins possess Nudix homology domains (NHDs) that have no known function. We show that NHDs are NAD+ (oxidized form of nicotinamide adenine dinucleotide) binding domains that regulate protein-protein interactions. The binding of NAD+ to the NHD domain of DBC1 (deleted in breast cancer 1) prevents it from inhibiting PARP1 [poly(adenosine diphosphate–ribose) polymerase], a critical DNA repair protein. As mice age and NAD+ concentrations decline, DBC1 is increasingly bound to PARP1, causing DNA damage to accumulate, a process rapidly reversed by restoring the abundance of NAD+. Thus, NAD+ directly regulates protein-protein interactions, the modulation of which may protect against cancer, radiation, and aging. [ABSTRACT FROM AUTHOR]

Background: Bacterivores, mostly represented by protists and nematodes, are a key component of soil biodiversity involved in soil fertility and plant productivity. In the current context of global change and soil biodiversity erosion, it becomes urgent to suitably recognize and quantify their ecological importance in ecosystem functioning. Scope: Using meta-analysis tools, we aimed at providing a quantitative synthesis of the ecological importance of soil bacterivores on ecosystem functions. We also intended to produce an overview of the ecological factors that are expected to drive the magnitude of bacterivore effects on ecosystem functions. Conclusions: Bacterivores in soil contributed significantly to numerous key ecosystem functions. We propose a new theoretical framework based on ecological stoichiometry stressing the role of C:N:P ratios in soil, microbial and plant biomass as important parameters driving bacterivore-effects on soil N and P availability for plants, immobilization of N and P in the bacterial biomass, and plant responses in nutrition and growth. [ABSTRACT FROM AUTHOR]

It has been hypothesised that aphid honeydew could alleviate the feeding damage by aphids via changes in soil biota leading to increased nutrient cycling and plant nutrient availability. However, to date, the evidence is equivocal. We used a field experiment with willow saplings to investigate the effect of aphid honeydew on trees with and without simulated honeydew deposition. Specifically, here we tested whether: (1) honeydew deposition can trigger changes in soil biota community composition, and (2) honeydew-induced changes in soil biota cascade up to affect plant performance and resource allocation. Honeydew deposition significantly increased microbial biomass and respiration, microfauna densities, earthworm biomass and litter mineralisation kinetics, while having detrimental effects on Collembola and mites. Honeydew deposition also increased the tree shoot to root biomass ratio and altered the crown canopy architecture and flowering phenology. However, no effects on leaf nitrogen content and tree shoot or root biomass were found. This was likely due to increased microbial nutrient immobilisation under the honeydew treatment. Path analyses present supporting evidence that the honeydew-induced changes in soil biota (notably via a pathway from microbial biomass to endogenic earthworms), can cascade up to affect tree resource allocation and crown architecture. [ABSTRACT FROM AUTHOR]

Mutations causing decreased somatotrophic signaling are known to increase insulin sensitivity and extend life span in mammals. Caloric restriction and every other day (EOD) dietary regimens are associated with similar improvements to insulin signaling and longevity in normal mice; however, these interventions fail to increase insulin sensitivity or life span in growth hormone receptor knockout (GHRKO) mice. To investigate the interactions of the GHRKO mutation with caloric restriction and EOD dietary interventions, we measured changes in the metabolic parameters oxygen consumption (VO2) and respiratory quotient produced by either long-term caloric restriction or EOD in male GHRKO and normal mice. GHRKO mice had increased VO2, which was unaltered by diet. In normal mice, EOD diet caused a significant reduction in VO2 compared with ad libitum (AL) mice during fed and fasted conditions. In normal mice, caloric restriction increased both the range of VO2 and the difference in minimum VO2 between fed and fasted states, whereas EOD diet caused a relatively static VO2 pattern under fed and fasted states. No diet significantly altered the range of VO2 of GHRKO mice under fed conditions. This provides further evidence that longevity-conferring diets cause major metabolic changes in normal mice, but not in GHRKO mice. [ABSTRACT FROM PUBLISHER]

The variation of individual life spans, even in highly inbred cohorts of animals and under strictly controlled environmental conditions, is substantial and not well understood. This variation in part could be due to epigenetic variation, which later affects the animal's physiology and ultimately longevity. Identification of the physiological properties that impact health and life span is crucial for longevity research and the development of anti-aging therapies. Here, we measured individual circadian and metabolic characteristics in a cohort of inbred F1 hybrid mice and correlated these parameters to their life spans. We found that mice with innate circadian periods close to 24 h (revealed during 30 days of housing in total darkness) enjoyed nearly 20% longer life spans than their littermates, which had shorter or longer innate circadian periods. These findings show that maintenance of a 24-h intrinsic circadian period is a positive predictor of longevity. Our data suggest that circadian period may be used to predict individual longevity and that processes that control innate circadian period affect aging. [ABSTRACT FROM AUTHOR]

By feeding on bacterial biomass protozoa play an acknowledged role in the liberation of nutrients in the plant rhizosphere. In addition there are suggestions that plants have mechanisms working through changes in root architecture and initiation of active release from soil organic matter, which are used to improve uptake and recirculation of nutrients in the ecosystem. All processes are carried out on a local scale in soil with roots, bacteria and protozoa interacting. The many actors and the small scale of interactions make experimentation diffi cult. We discuss mistakes, pitfalls and misinterpretations and provide suggestions for improvement. Recent methodological progress has opened new exciting avenues for protozoan research. New techniques have already helped to reveal protozoan regulation of cooperation as well as confl ict in bacterial communities. These mechanisms in turn affect bacterial functioning and target molecular control points in rhizosphere food webs in relation to plants. Integrating nutritional and regulatory aspects into new concepts of protozoan functioning in soil is a challenging frontier in protozoology. [ABSTRACT FROM AUTHOR]

In alpine zones, soil microbial biomass and activity are strongly dependent on the seasonal snow cover. Current models assume that microbial biomass reaches an annual peak in winter under the insulating snowpack with a subsequent sharp decline during snowmelt. In this study, we investigated the seasonal dynamics of the soil microbial biomass in the Central Alps, where usually early snowfall buffers winter soil temperatures. We conducted a large-scale survey in three mountains around Davos (Switzerland) along altitudinal gradients from approximately 1900 to 2800 m above sea level. Using a space-for-time approach during snowmelt, soil samples were taken (1) under, (2) at the edge of, and (3) one meter away from remaining snow patches. One additional sample per site was taken in summer to further evaluate the seasonal dynamics. In total, 184 soil samples from 46 different sites were analyzed. We measured microbial biomass C and N, enzymatic activity and dissolved C and N. We observed an increase of microbial biomass and dissolved C during and immediately after snowmelt, as well as an increase from spring to summer. We suggest that the absence of soil freezing in winter and the growing amounts of dissolved C supported a continued growth, without a sudden collapse of the microbial biomass. Our results underline the importance of the insulating effect of the seasonal snow cover for the microbial dynamics. Global warming is modifying the timing and abundance of the seasonal snow cover, and our results will help to refine models for the dynamics of soil microbes in alpine ecosystems. [ABSTRACT FROM AUTHOR]

Abstract: The effects of a simple decomposer community, consisting of collembola, enchytraeids and earthworms on the performance of plants in a model Mediterranean early successional grassland community were investigated. Interactions of plant functional groups and species within the soil decomposer community resulted in significant shifts of plant competitive strength and therefore are likely to affect the rate of the successional development of plant communities. Depending on the functional role of the decomposer taxa involved, either legumes, or non-leguminous forbs were more negatively affected. Therefore, increasing species numbers with in the decomposer community gradually reduced the relative contribution of forbs (legumes and non-leguminous forbs), although fundamentally different mechanisms were responsible for these effects. Surprisingly, not the biomass-dominant annelid taxa, but collembola had the strongest effects on plant performance. The grass-to-forb ratio, an indicator of successional change, shifted from 3 to 4 in presence of collembola, suggesting that indirect effects on microbial symbionts of plants were more important than classic decomposer effects via increased and more constant nutrient availability to plants. Total plant productivity, however, was not affected, since grasses gained competitive advantage and compensated with increased growth for the negative animal effects on forb performance. Our results highlight the importance of specific functional groups among decomposers for structuring grassland plant communities. However, great plasticity in the plant community through negative covariance between forbs and grasses, partly compensated for decomposer effects at the plant canopy level. [Copyright &y& Elsevier]

The interaction of longevity-conferring genes with longevity-conferring diets is poorly understood. The growth hormone receptor gene-disrupted (GHR-KO) mouse is long lived; and this longevity is not responsive to 30% caloric restriction, in contrast to wild-type animals from the same strain. To determine whether this may have been limited to a particular level of dietary restriction, we subjected GHR-KO mice to a different dietary restriction regimen, an intermittent fasting diet. The intermittent fasting diet increased the survivorship and improved insulin sensitivity of normal males, but failed to affect either parameter in GHR-KO mice. From the results of two paradigms of dietary restriction, we postulate that GHR-KO mice would be resistant to any manner of dietary restriction; potentially due to their inability to further enhance insulin sensitivity. Insulin sensitivity may be a mechanism and/or a marker of the lifespan extending potential of an intervention. [ABSTRACT FROM AUTHOR]

Growth hormone (GH) signaling influences longevity in mice, with decreased GH signaling associated with longer life span and increased GH signaling with shortened life span. A proposed mechanism through which GH signaling influences life span postulates that decreased GH signaling towers metabolic rate, thus slowing aging by decreasing production of damaging free radicals. The influence of altered GH signaling on metabolism was tested by monitoring oxygen consumption (VO2), respiratory quotient (RQ), and heat production in long-lived GH receptor knockout (GHRKO) and Ames dwarf mice, and short-lived bovine GH-overexpressing transgenic (bGH TG) mice. Intriguingly, both GHRKO and Ames dwarf mice have increased VO2 and heat per gram body weight, and decreased RQ, whereas bGH TG mice have decreased VO2 and heat per gram body weight and increased RQ. In conclusion, decreased GH signaling associates with increased metabolism per body weight and may beneficially affect mitochondrial flexibility by increasing the capacity for fat oxidation; generally, GH excess produces opposite metabolic effects. [ABSTRACT FROM AUTHOR]

Most mutations that delay aging and prolong lifespan in the mouse are related to somatotropic and/or insulin signaling. Calorie restriction (CR) is the only intervention that reliably increases mouse longevity. There is considerable phenotypic overlap between long-lived mutant mice and normal mice on chronic CR. Therefore, we investigated the interactive effects of CR and targeted disruption or knock out of the growth hormone receptor (GHRKO) in mice on longevity and the insulin signaling cascade. Every other day feeding corresponds to a mild (i.e. 15%) CR which increased median lifespan in normal mice but not in GHRKO mice corroborating our previous findings on the effects of moderate (30%) CR on the longevity of these animals. To determine why insulin sensitivity improves in normal but not GHRKO mice in response to 30% CR, we conducted insulin stimulation experiments after one year of CR. In normal mice, CR increased the insulin stimulated activation of the insulin signaling cascade (IR/IRS/PI3K/AKT) in liver and muscle. Livers of GHRKO mice responded to insulin by increased activation of the early steps of insulin signaling, which was dissipated by altered PI3K subunit abundance which putatively inhibited AKT activation. In the muscle of GHRKO mice, there was elevated downstream activation of the insulin signaling cascade (IRS/PI3K/AKT) in the absence of elevated IR activation. Further, we found a major reduction of inhibitory Ser phosphorylation of IRS-1 seen exclusively in GHRKO muscle which may underpin their elevated insulin sensitivity. Chronic CR failed to further modify the alterations in insulin signaling in GHRKO mice as compared to normal mice, likely explaining or contributing to the absence of CR effects on insulin sensitivity and longevity in these long-lived mice. [ABSTRACT FROM AUTHOR]

Abstract: We investigated microbial biomass, fungal biomass and microbial community structure at three altitudes (1000, 2000 and 3000m) and in two soil layers [L/F layer (Layer I) and underlying H/Ah layer (Layer II)] of tropical mountain rain forests in southern Ecuador. Basal respiration, microbial biomass and concentration of ergosterol generally declined from Layer I to Layer II and peaked at 2000m. Compared to temperate forest ecosystems microbial biomass and ergosterol concentrations were generally low. Patterns in phospholipid fatty acids indicated that the composition of microbial communities markedly changed from Layer I to Layer II. These differences between layers decreased with increasing altitude. The concentration of the arbuscular mycorrhizal fungal marker PLFA 16:1ω5c decreased with altitude in Layer I but increased in Layer II. The fungal-to-bacterial ratio increased with altitude and was higher in Layer I than in Layer II. Presumably, low microbial biomass in soils of tropical forest ecosystems is due to high temperature associated with high respiration but also low litter quality, with the latter declining with altitude. These conclusions are supported by the fact that at higher altitude the microbial community changed from a bacterial-dominated to a fungal-dominated system. CCA showed that microbial biomass correlated closely with density of a number of putatively bacterial feeding testate amoeba species including Corythion dubium Taranek, 1871, Euglypha cristata Leidy, 1879, Trigonopyxis arcula Penard, 1912, Tracheleuglypha dentata Deflandre, 1928 and Trinema lineare Penard, 1890. Ergosterol concentrations, but not the PLFA 18:2ω6c, strongly correlated with the putatively fungal feeding species Phryganella acropodia (Hertwig, Lesser, 1874) Hopkinson, 1909. Generally, parallel to microbial biomass and ergosterol concentrations the density of testate amoebae peaked at 2000m. However, compared to microbial parameters changes in testate amoebae communities between two layers were less pronounced. The data suggest that density and community structure of testate amoebae are driven by the availability of food resources (bacteria and fungi) which at high altitude decrease with increasing moisture and decreasing pH. [Copyright &y& Elsevier]

Calorie restriction (CR) improves insulin sensitivity and increases life span in normal but not in long-lived growth hormone-resistant knockout (GHRKO) mice. In this study, we examined interactive effects of GH resistance and long-term CR on cardiac insulin action. GHRKO mice exhibited marked increases in the insulin-induced phosphorylation of the insulin receptor (IR), insulin receptor substrate-1 (IRS-1), Akt, and ERK1/2 along with elevated insulin-stimulated IRS-1-associated regulatory subunit of phosphatidylinositol 3-kinase in the heart. These changes were associated with elevated protein levels of IR, IRS-1, and Akt and with a down-regulation of cardiac glucose transporter 4 (GLUT4). In normal mice, CR induced an important increase in the phosphorylation of cardiac Akt without elevation of Akt protein, reaching activation levels similar to those seen in GHRKO mice. This change may be cardioprotective and thus contribute to increased longevity in response to CR. Interestingly, the insulin signaling cascade in the heart of GHRKO mice was unaffected by CR. [ABSTRACT FROM AUTHOR]

Summary: We investigated the species composition of testate amoebae at three altitudes (1000, 2000 and 3000m) and two horizons (L and F/H/Ah) of a tropical mountain rain forest in southern Ecuador. A total of 135 species and intraspecific taxa of testate amoebae were found (36 samples). Rarefaction plots suggest that only few more species are to be expected. Species number in the L horizon was at a maximum at 2000m (109 species) and similar at 1000 and 3000m (75 and 71 species, respectively). Species numbers in the F/H/Ah horizon were 29, 67 and 48 at 1000, 2000 and 3000m, respectively. The density of testate amoebae in the L horizon increased significantly in the order 1000<3000<2000m with 3147±129, 9198±144 and 12,497±1317ind.g−1 dry matter and in the F/H/Ah horizon with 176±25, 3118±97 and 4986±102ind.g−1 dry matter, respectively. The significant Horizon×Elevation interaction reflects the exceptionally low abundance of testate amoebae in the Ah horizon at 1000m. The results suggest that species richness of testate amoebae does not decrease continuously with elevation; rather, it peaks at an intermediate elevation. Further, the data suggest that diversity, but not density of testate amoebae in tropical forests exceeds that in temperate forests. Morphological features of testate amoebae reflected semiaquatic habitat conditions. The great majority of testate amoebae species of the studied tropical mountain rain forests are geographically widespread, including temperate regions; however 9 of the species (i.e. 6.7%) are considered tropical, some of these species likely represent Gondwana relicts. [Copyright &y& Elsevier]

There is conflicting information on the physiological role of growth hormone (GH) in the control of aging. This study reports dual-energy x-ray absorptiometry (DXA) measurements of body composition and bone characteristics in young, adult, and aged long-lived GH receptor knockout (GHR-KO) and normal mice to determine the effects of GH resistance during aging. Compared to controls. GHR-KO mice showed an increased percentage of body lat. GHR-KO mice have reduced total-body bone mineral density (BMD), bone mineral content, and bone area, but these parameters increased with age. In addition, GHR-KO mice have decreased femur length, femur BMD, and lower lumbar BMD compared to controls in all age groups. These parameters also continued to increase with age. Our results indicate that GH resistance alters body composition, bone growth, and bone maintenance during aging in GHR-KO mice [ABSTRACT FROM AUTHOR]

Reduced intake of nutrients [calorie restriction (CR)] extends longevity in organisms ranging from yeast to mammals. Mutations affecting somatotropic, insulin, or homologous signaling pathways can increase life span in worms, flies, and mice, and there is considerable evidence that reduced secretion of insulin-like growth factor I and insulin are among the mechanisms that mediate the effects of CR on aging and longevity in mammals. In the present study, mice with targeted disruption of the growth hormone (GH) receptor EGH receptor/GH-binding protein knockout (GHRKO) mice] and their normal siblings were fed ad libitum (AL) or subjected to 30% CR starting at 2 months of age. In normal females and males, CR produced the expected increases in overall, average, median, and maximal life span. Longevity of normal mice subjected to CR resembles that of GHRKO animals fed AL. In sharp contrast to its effects in normal mice, CR failed to increase overall, median, or average life span in GHRKO mice and increased maximal life span only in females. In a separate group of animals, CR for 1 year improved insulin sensitivity in normal mice but failed to further enhance the remarkable insulin sensitivity in GHRKO mutants. These data imply that somatotropic signaling is critically important not only in the control of aging and longevity under conditions of unlimited food supply but also in mediating the effects of CR on life span. The present findings also support the notion that enhanced sensitivity to insulin plays a prominent role in the actions of CR and GH resistance on longevity. [ABSTRACT FROM AUTHOR]

A gradient of microbial diversity in soil was established by inoculating pasteurized soil with microbial populations of different complexity, which were obtained by a combination of soil fumigation and filtering techniques. Four different soil diversity treatments were planted with six different grass species either in monoculture or in polyculture to test how changes of general microbial functions, such as catabolic diversity and nutrient recycling efficiency would affect the performance of the plant communities. Relatively harsh soil treatments were necessary to elicit visible effects on major soil processes such as decomposition and nitrogen cycling due to the high redundancy and resilience of soil microbial communities. The strongest effects of soil diversity manipulations on plant growth occurred in polycultures where interspecific competition between plants was high. In polycultures, soil diversity reduction led to a gradual, linear decline in biomass production of one subordinate grass species (Bromus hordeaceus), which was compensated by increased growth of two intermediate competitors (Aegilops geniculata,B. madritensis). This negative covariance in growth of competing grass species smoothed the effects of soil diversity manipulations at the plant community level. As a result, total shoot biomass production remained constant. Apparently the effects of soil diversity manipulations were buffered because functional redundancy at both, the microbial and the plant community level complemented each other. The results further suggests that small trade-offs in plant fitness due to general functional shifts at the microbial level can be significant for the outcome of competition in plant communities and thus diversity at much larger scales. [ABSTRACT FROM AUTHOR]

Decomposer animals stimulate plant growth by indirect effects such as increasing nutrient availability or by modifying microbial communities in the rhizosphere. In grasslands, the spatial distribution of organic matter (OM) rich in nutrients depends on agricultural practice and the bioturbation activities of large detritivores, such as earthworms. We hypothesized that plants of different functional groups with contrasting nutrient uptake and resource allocation strategies differentially benefit from sites in soil with OM accumulation and the presence of decomposer animals. In a greenhouse experiment we investigated effects of spatial distribution of 15N-labelled grass litter, earthworms and collembola on a simple grassland community consisting of Lolium perenne (grass) and Trifolium repens (legume). Litter aggregates (compared to homogeneous litter distribution) increased total shoot biomass, root biomass and 15N uptake by the plants. Earthworms and collembola did not affect total N uptake of T. repens; however, the presence of both increased 15N uptake by T. repens and L. perenne. Earthworms increased shoot biomass of T. repens 1.11-fold and that of L. perenne 2.50 fold. Biomass of L. perenne was at a maximum in the presence of earthworms, collembola and with litter concentrated in a single aggregate. Shoot biomass of T. repens increased in the presence of collembola, with L. perenne generally responding opposingly. The results indicate that the composition of the decomposer community and the distribution of OM in soil affect plant competition and therefore plant community composition. [Copyright &y& Elsevier]

Summary Acknowledgements References All nutrients that plants absorb have to pass a region of intense interactions between roots, microorganisms and animals, termed the rhizosphere. Plants allocate a great portion of their photosynthetically fixed carbon to root-infecting symbionts, such as mycorrhizal fungi; another part is released as exudates fuelling mainly free-living rhizobacteria. Rhizobacteria are strongly top-down regulated by microfaunal grazers, particularly protozoa. Consequently, beneficial effects of protozoa on plant growth have been assigned to nutrients released from consumed bacterial biomass, that is, the ‘microbial loop’. In recent years however, the recognition of bacterial communication networks, the common exchange of microbial signals with roots and the fact that these signals are used to enhance the efflux of carbon from roots have revolutionized our view of rhizosphere processes. Most importantly, effects of rhizobacteria on root architecture seem to be driven in large by protozoan grazers. Protozoan effects on plant root systems stand in sharp contrast to effects of mycorrhizal fungi. Because the regulation of root architecture is a key determinant of nutrient- and water-use efficiency in plants, protozoa provide a model system that may considerably advance our understanding of the mechanisms underlying plant growth and community composition. © New Phytologist (2004) doi: 10.1111/j.1469-8137.2004.01066.x [ABSTRACT FROM AUTHOR]

We investigated if the activity of soil invertebrates (protozoa and earthworms) affected the performance of barley and if effects propagated higher up the above-ground food chain into herbivores (cereal aphid, Sitobion avenae ). Barley plants were grown individually in microcosms containing defaunated soil and grass residues. Plants were grown in soil containing: a) no added fauna, b) protozoa, c) earthworms, or d) protozoa and earthworms. After 7 weeks growth at 20°C three adult cereal aphids were added to each plant on separate leaves. The aphids were allowed to grow and reproduce for another 2 weeks before the experiment was destructively sampled. Amounts of mineral N in the soil and leached from the microcosms were significantly reduced by the presence of soil animals. Correspondingly plant biomass and total plant N content were increased significantly by soil animals, protozoa in particular. The different mechanisms responsible for changes in nutrient turnover in presence of protozoa and earthworms are discussed. Aphid performance was strongly influenced by the presence of protozoa, but not by earthworms. In the presence of protozoa the numbers and biomass of adult and juvenile aphids were significantly increased. These effects are likely due to an increased N content in barley plants and consequently increased nitrogen availability to aphids. The results underline that the detritivore and herbivore systems are intimately linked. [ABSTRACT FROM AUTHOR]

Protists, a crucial part of the soil food web, are increasingly acknowledged as significant influencers of nutrient cycling and plant performance in farmlands. While topographical and climatic factors are often considered to drive microbial communities on a continental scale, higher trophic levels like heterotrophic protists also rely on their food sources. In this context, bacterivores have received more attention than fungivores. Our study explored the connection between the community composition of protists (specifically Rhizaria and Cercozoa) and fungi across 156 cereal fields in Europe, spanning a latitudinal gradient of 3000 km. We employed a machine‐learning approach to measure the significance of fungal communities in comparison to bacterial communities, soil abiotic factors, and climate as determinants of the Cercozoa community composition. Our findings indicate that climatic variables and fungal communities are the primary drivers of cercozoan communities, accounting for 70% of their community composition. Structural equation modelling (SEM) unveiled indirect climatic effects on the cercozoan communities through a change in the composition of the fungal communities. Our data also imply that fungivory might be more prevalent among protists than generally believed. This study uncovers a hidden facet of the soil food web, suggesting that the benefits of microbial diversity could be more effectively integrated into sustainable agriculture practices. [ABSTRACT FROM AUTHOR]

Abstract: Fluorescent pseudomonads show great potential as biological control agents due to their capability to produce antifungal toxins such as 2,4-diacetylphloroglucinol (DAPG). DAPG is synthesized from the precursor monoacetyl-phloroglucinol (MAPG) and its production depends on the metabolic state of the bacteria as well as on their interaction with other organisms. In this study we show that Pseudomonas fluorescens responds to the bacterivorous amoeba Acanthamoeba castellanii by upregulating the production of phloroglucinol derivates in a density-dependent manner. Living amoebae caused moreover a distortion of the MAPG to DAPG balance in favor of the latter, suggesting that amoebae may interfere with the first steps of DAPG synthesis. Predator–prey interactions appear thus to be an important factor for the regulation of antibiotics production in biocontrol microorganisms. [Copyright &y& Elsevier]

Soil microbial C:N:P stoichiometry and microbial maintenance respiration (i.e. metabolic quotient, qCO2) were monitored along a nutrient gradient in soils from a 52-year space-for-time chronosequence of reclaimed agricultural land after brown-coal mining. Land reclamation produced loess soils of initially low (0.2%) SOC. Consecutive agricultural land management led to a gradual recovery of SOC contents. Our data revealed sudden shifts in microbial stoichiometry and metabolic quotient with increasing SOC at a critical value of 1% SOC. As SOC increased, accrual rate of C into microbial biomass decreased, whereas microbial N increased. Simultaneously, metabolic quotient strongly decreased with increasing SOC until the same critical value of 1% SOC and remained at a constant low thereafter. The microbial fractions of the soil in samples containing < 1% SOC were out of stoichiometric equilibrium and were inefficient at immobilising C due to high maintenance respiration. Increasing SOC above the threshold value shifted the soil microbes towards a new equilibrium where N became growth limiting, leading to a more efficient acquisition of C. The shift in microbial N accrual was preluded by high variation in microbial biomass N in soils containing 0.5–0.9% SOC indicative of a regime shift between microbial stoichiometric equilibria. Our data may help in establishing a quantitative framework for SOC targets that, along with agricultural intensification, may better support feedback mechanisms for a sustainable accrual of C in soils. [ABSTRACT FROM AUTHOR]

About a thousand described species of Myxomycetes, colloquially named slime moulds, are present in most terrestrial habitats. Molecular environmental sampling has revealed that a significant proportion of sequences could not be assigned to known species, with some specific groups showing a high hidden diversity. One such group included Stemonitis and allied genera, with only a few closely related reference sequences from known species and many distantly related sequences from environmental sampling. To improve the phylogeny and help define genera in this lineage, we provided nine new small-subunit ribosomal RNA gene sequences of Stemonitis and allied genera, along with microscopy observations. We showed that the genus Stemonitis is polyphyletic, clearly separated into two groups, with the main distinguishing feature being spore ornamentation. The first group included the type species Stemonitis fusca, and was characterized by reticulated spores, while the second contained species with warted spores (e.g. S. flavogenita and S. axifera) and many undetermined environmental sequences. In addition, we show that the related genera Stemonitopsis, Stemonaria and Symphytocarpus were polyphyletic and that their circumscription was based on inconsistent characteristics. Instead, representatives of these genera clustered into the two clades according to their spore ornamentation. Our study provides a first insight into the genetic diversity of Stemonitis and allied genera, and proposes spore ornamentation as an evolutionary informative feature to distinguish genera in this group. [ABSTRACT FROM AUTHOR]

Thecofilosea is a class in Cercozoa (Rhizaria) comprising mainly freshwater‐inhabiting algivores. Recently, numerous isolates of thecofilosean amoebae have been cultured and were characterized by an integrated morphological and molecular approach. As attempts to establish a culture of Lecythium mutabilis repeatedly failed, it was not yet investigated by molecular means. We isolated single cells of L. mutabilis directly from their habitat and successfully sequenced the V4 region of their SSU rDNA. Phylogenetic analyses showed that L. mutabilis is not directly related to the genus Lecythium and instead branches within the Fiscullidae (Tectofilosida, Thecofilosea). Accordingly, we transfer the species L. mutabilis to a novel genus Omnivora gen. nov. [ABSTRACT FROM AUTHOR]

Aim: Depending on the availability and stoichiometry of nutrients in soil, microbes and plants can compete for the same resources. In this study we aimed to test how microbial nutrient limitation in agricultural systems can be linked to fertilizer regimes and sugar beet yield. Methods: We measured the dynamics of microbial growth responses by monitoring soil respiration after the application of carbon (C), C and nitrogen (N), C and phosphorus (P) and C, N and P to soils of an agricultural long-term fertilization experiment in Speyer (Germany). Samples were taken in February and June before harvest and in November after harvest. Results: CN limitation in June was the best predictor for sugar beet yield, with increasing CN limitation there was a decreasing yield. Mineral N fertilization in May alleviated microbial N limitation in June. Over the course of the sampling, microbial nutrient limitations were highest after harvest in November. Conclusions: Together, our results indicate that plants and microbes compete for the same nutrients, and that plants are more competitive at acquiring them. Measurements of microbial nutrient limitation four months before harvest successfully predicted sugar beet yield and could therefore be used as a diagnostic indicator. [ABSTRACT FROM AUTHOR]

Summary: Plants impact the development of their rhizosphere microbial communities. It is yet unclear to what extent the root cap and specific root zones contribute to microbial community assembly.To test the roles of root caps and root hairs in the establishment of microbiomes along maize roots (Zea mays), we compared the composition of prokaryote (archaea and bacteria) and protist (Cercozoa and Endomyxa) microbiomes of intact or decapped primary roots of maize inbred line B73 with its isogenic root hairless (rth3) mutant. In addition, we tracked gene expression along the root axis to identify molecular control points for an active microbiome assembly by roots.Absence of root caps had stronger effects on microbiome composition than the absence of root hairs and affected microbial community composition also at older root zones and at higher trophic levels (protists). Specific bacterial and cercozoan taxa correlated with root genes involved in immune response.Our results indicate a central role of root caps in microbiome assembly with ripple‐on effects affecting higher trophic levels and microbiome composition on older root zones. [ABSTRACT FROM AUTHOR]

Two new species of Copris Geoffroy, 1762 are described and illustrated: Copris (subgenus incertae sedis) caobangensis sp. n. from Caobang Province (northern Vietnam) and Copris (Copris) sonensis sp. n. from Thanhhoa Province (central Vietnam). Copris (Copris) szechouanicus Balthasar, 1958 is recorded in Vietnam for the fi rst time and data on the morphology, distribution and ecology of this species are given. An updated species list and an identifi cation key for the Copris species so far known from Vietnam are presented along with detailed photographs of the poorly known species. [ABSTRACT FROM AUTHOR]

Two new species of Copris Geoffroy, 1762 are described and illustrated: Copris (subgenus incertae sedis) caobangensis sp. n. from Caobang Province (northern Vietnam) and Copris (Copris) sonensis sp. n. from Thanhhoa Province (central Vietnam). Copris (Copris) szechouanicus Balthasar, 1958 is recorded in Vietnam for the first time and data on the morphology, distribution and ecology of this species are given. An updated species list and an identification key for the Copris species so far known from Vietnam are presented along with detailed photographs of the poorly known species. [ABSTRACT FROM AUTHOR]

Preferential food selection in protists is well documented, but we still lack basic understanding on how protist predation modifies the taxonomic and functional composition of bacterial communities. We conducted feeding trials using leaf-associated cercomonad Cercozoa by incubating them on a standardized, diverse bacterial community washed from plant leaves. We used a shotgun metagenomics approach to investigate the taxonomic and functional changes of the bacterial community after five days protist predation on bacteria. Predation-induced shifts in bacterial community composition could be linked to phenotypic protist traits. Protist reproduction rate, morphological plasticity and cell speed were most important in determining bacterial community composition. Analyses of co-occurrence patterns showed less complex correlations between bacterial taxa in the protist-grazed treatments with a higher proportion of positive correlations than in non-grazed controls, suggesting that predation reduced the influence of strong competitors. Protist predation influenced 14 metabolic core functions including membrane transport from which type VI secretion systems were in particular upregulated. In view of the functional importance of bacterial communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of predator-prey interactions, changes in microbial composition and function, and subsequent repercussions on plant performance are clearly required. [ABSTRACT FROM AUTHOR]

Interactions occur between two or more organisms affecting each other. Interactions are decisive for the ecology of the organisms. Without direct experimental evidence the analysis of interactions is difficult. Correlation analyses that are based on co-occurrences are often used to approximate interaction. Here, we present a new mathematical model to estimate the interaction strengths between taxa, based on changes in their relative abundances across environmental gradients. [ABSTRACT FROM AUTHOR]

Thecofilosea is a class in Cercozoa comprising mainly freshwater inhabiting algivores. Since direct observation of amoeboid protists in soil is not possible, the prey spectra of their terrestrial relatives remain obscure. To test for grazing selectivity and the preferred prey of terrestrial thecofiloseans, we conducted a food choice experiment including yeasts and algae as prey. When being offered all food sources at once, the yeast cells were strongly reduced, whereas the abundance of the algae only slightly decreased. Since Fisculla terrestris thrives with fungal prey, it must be considered as a predator of eukaryotes with high preference for fungal cells. [ABSTRACT FROM AUTHOR]

Protists are abundant, diverse and perform essential functions in soils. Protistan community structure and its change across time or space are traditionally studied at the species level but the relative importance of the processes shaping these patterns depends on the taxon phylogenetic resolution. Using 18S rDNA amplicon data of the Cercozoa, a group of dominant soil protists, from an agricultural field in western Germany, we observed a turnover of relatively closely related taxa (from sequence variants to genus‐level clades) across soil depth; while across soil habitats (rhizosphere, bulk soil, drilosphere), we observed turnover of relatively distantly related taxa, confirming Paracercomonadidae as a rhizosphere‐associated clade. We extended our approach to show that closely related Cercozoa encounter divergent arbuscular mycorrhizal (AM) fungi across soil depth and that distantly related Cercozoa encounter closely related AM fungi across soil compartments. This study suggests that soil Cercozoa community assembly at the field scale is driven by niche‐based processes shaped by evolutionary legacy of adaptation to conditions primarily related to the soil compartment, followed by the soil layer, giving a deeper understanding on the selection pressures that shaped their evolution. [ABSTRACT FROM AUTHOR]

Aims: Different drivers are known to shape rhizosphere microbiome assembly. How soil texture (Texture) and presence or lack of root hairs (Root Hair) of plants affect the rhizosphere microbiome assembly and soil potential extracellular enzyme activities (EEA) at defined rooting depth (Depth) is still a knowledge gap. We investigated effects of these drivers on microbial assembly in rhizosphere and on potential EEA in root-affected soil of maize. Methods: Samples were taken from three depths of root hair defective mutant rth3 and wild-type WT maize planted on loam and sand in soil columns after 22 days. Rhizosphere bacterial, archaeal, fungal and cercozoan communities were analysed by sequencing of 16S rRNA gene, ITS and 18S rRNA gene fragments. Soil potential EEA of ß-glucosidase, acid phosphatase and chitinase were estimated using fluorogenic substrates. Results: The bacterial, archaeal and cercozoan alpha- and beta-diversities were significantly and strongly altered by Texture, followed by Depth and Root Hair. Texture and Depth had a small impact on fungal assembly, and only fungal beta-diversity was significantly affected. Significant impacts by Depth and Root Hair on beta-diversity and relative abundances at taxonomic levels of bacteria, archaea, fungi and cercozoa were dependent on Texture. Likewise, the patterns of potential EEA followed the trends of microbial communities, and the potential EEA correlated with the relative abundances of several taxa. Conclusions: Texture was the strongest driver of rhizosphere microbiome and of soil potential EEA, followed by Depth and Root Hair, similarly to findings in maize root architecture and plant gene expression studies. [ABSTRACT FROM AUTHOR]

Myxomycetes or plasmodial slime molds are widespread and very common soil amoebae with the ability to form macroscopic fruiting bodies. Even if their phylogenetic position as a monophyletic group in Amoebozoa is well established, their internal relationships are still not entirely resolved. At the base of the most intensively studied dark-spored clade lies the order Echinosteliales, whose highly divergent small subunit ribosomal (18S) RNA genes represent a challenge for phylogenetic reconstructions. This is because they are characterized by unusually long variable helices of unknown secondary structure and a high inter- and infraspecific divergence. Current classification recognizes two families: the monogeneric Echinosteliaceae and the Clastodermataceae with the genera Barbeyella and Clastoderma. To better resolve the phylogeny of the Echinosteliales, we obtained three new small subunit ribosomal (18S) RNA gene sequences of Clastoderma and Echinostelium corynophorum. Our phylogenetic analyses suggested the polyphyly of the family Clastodermataceae, as Barbeyella was more closely related to Echinostelium arboreum than to Clastoderma, while Clastoderma debaryanum was the earliest branching clade in Echinosteliales. We also found that E. corynophorum was the closest relative of the enigmatic Semimorula liquescens, a stalkless-modified Echinosteliales. We discuss possible evolutionary pathways in dark-spored Myxomycetes and propose a taxonomic update. [ABSTRACT FROM AUTHOR]

A new species, the third one from Vietnam, of the genus Aporcelinus is described from natural areas. Aporcelinus falcicaudatus sp. n. is characterized by its 1.28 to 1.63 mm long body, lip region offset by weak constriction and 16 to 18 µm broad, odontostyle 18 to 21 µm at its ventral side, neck 354 to 406 µm long, uterus tripartite and 61 to 95 mm long, V = 50 to 55, tail strongly recurved dorsad and conical (23-31 µm, c = 43-58, c' = 0.7-0.9) with finely rounded tip, and male absent. Scanning electron microscope (SEM) study, the first of a representative of the genus, shows a lip region pattern significantly different from that observed in the typical aporcelaimid taxa. [ABSTRACT FROM AUTHOR]

The analysis of 18S rRNA gene amplicons is an important tool to characterize the diversity of the eukaryotic soil microbiome. Here we analyzed two primer sets (TAReuk, EKeuk) and the impact of a newly designed antifungal peptide nucleic acid to enhance the detection of protists in silico and with soil DNA extracted from croplands and a forest. The in silico analyses showed for TAReuk pronounced specificities for protist SAR supergroup and Metazoa, while EKeuk was particularly specific for Ascomycota and Basidiomycota. In silico , the PNA matched with the majority of Ascomycota (81.3 %) and Basidiomycota (65.4 %), but with <6 % of protists. The contrasting primer specificities were confirmed with soil DNA, but the proportion of protist amplicons was similar. In contrast to in silico , effects of the PNA were not as clear with soil DNA, even though it completely inhibited the amplification of the targeted fungal sequences. PNA effects were more pronounced with TAReuk, and results with cropland and forest soil DNA were not consistent, e.g. , for cropland, PNA decreased the relative abundance of fungi but for forest it was the opposite, possibly because of different fungal diversity. The divergence between PNA in silico -predictions and results with soil DNA are likely an outcome of primer binding to <100 % complementary target sequences and a still limited DNA sequence databases for soil microbial eukaryotes. With TAReuk, the presence of PNA enhanced the detection of Conosa and, thus, could be a useful tool to study this group in the future. • A new PNA probe inhibited in silico PCR amplification of most fungal 18S rRNA genes. • With soil DNA, the PNA probe did not inhibit amplification of fungal 18S rRNA genes. • PNA effects on detection of protists varied between two 18S rRNA primer pairs. • PNA effects varied between DNA extracted from five different soils. • With the common TAReuk, protist primers PNA increased the detection of Conosa. [ABSTRACT FROM AUTHOR]

Determining the influence of climate in driving the global distribution of soil microbial communities is fundamental to help predict potential shifts in soil food webs and ecosystem functioning under global change scenarios. Herein, we used a global survey including 80 dryland ecosystems from six continents, and found that the relative abundance of ecological clusters formed by taxa involved in bacteria-fungi and bacteria-cercozoa bipartite networks was highly sensitive to changes in temperature and aridity. Importantly, such a result was maintained when controlling for soil, geographical location and vegetation attributes, being pH and soil organic carbon important determinants of the relative abundance of the ecological clusters. We also identified potential global associations between important soil microbial taxa, which can be useful to support the conservation of terrestrial ecosystems under global change scenarios. Our results suggest that increases in temperature and aridity such as those forecasted for the next decades in drylands could potentially lead to drastic changes in the community composition of functionally important bipartite networks within soil food webs. This could have important but unknown implications for the provision of key ecosystem functions and associated services driven by the organisms forming these networks if other taxa cannot cope with them. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'. [ABSTRACT FROM AUTHOR]

Climate change is considered to negatively affect vertebrate biodiversity. Lizards in tropical regions are considered particularly vulnerable due to their narrow temperature tolerances. The crocodile lizard Shinisaurus crocodilurus , an ecologically specialized semiaquatic species, is under the risk of extinction due to habitat loss and overharvesting. It is only found in isolated relict populations in southern China and northern Vietnam. Data on the thermal niche of the species are crucial to assess its vulnerability to climatic changes. We developed a backpack system with temperature data loggers for S. crocodilurus in order to monitor the lizard's temperature preferences in its natural habitat in Vietnam. We found that S. crocodilurus vietnamensis preferred a mean ambient temperature range of 24 ± 1°C (min-max: 22-31°C) at natural habitat sites, a far lower temperature amplitude compared to the recorded ambient temperature range at habitat sites. In its natural habitat, S. crocodilurus vietnamensis avoided in particular high temperatures, indicating the importance of constantly cool streams and intact vegetation for the provision of shade and shelter. We further provide first insights into the seasonal variation in microhabitat use and activity of S. crocodilurus vietnamensis based on data from individuals kept in outdoor enclosures under natural climatic conditions in Vietnam, collected daily over a period of eight months. Our results aim to aid further conservation measures for the species, such as the identification and protection of core habitat sites and sites for restocking, as well as to adjust and improve conservation breeding programs for the species. [ABSTRACT FROM AUTHOR]