Functional diversity and community structure of micro-organisms in three arctic soils as determined by sole-carbon-source-utilization

Functional diversities of micro-organisms in arctic soils at three incubation temperatures were assessed using sole-carbon-source-utilization (SCSU). Soil samples were collected from an area of anthropogenic fertilization (mixed Dorset/Thule/Historic site), an area of animal enrichment (bird rock perches), and unaltered tundra (raised beach; control soil site). The micro-organisms were extracted from the soil samples and inoculated into Gram-negative (GN) Biolog plates incubated at 30°C, 10°C, and 4°C. Calculations of the Shannon index, substrate utilization richness, Shannon evenness, and the Jaccard coefficient of similarity were based upon substrate utilization on the Biolog plates. Principal component analysis distinguished microbial communities in enriched soils from unenriched soils. At 10°C and 4°C, Shannon indices of enriched soil microbial communities (10°C: soils influenced by wild animals=4.28, soils influenced by human activities=4.20; 4°C: soils influenced by wild animals=4.15, soils influenced by human activities=4.03) were significantly higher than unenriched soil microbial communities (10°C: 3.66; 4°C: 3.38). Substrate utilization richness and evenness displayed similar trends. Although Jaccard coefficients showed uniformity across the different soil samples, cluster analysis supported patterns demonstrated by PCA. Lower temperatures (4°C and 10°C) yielded greater resolution between soil microbial communities than 30°C based on Biolog colour development patterns.     

The hormone-sensitive lipase from Psychrobacter sp. TA144: New insight in the structural/functional characterization

Cold-adapted esterases and lipases have been found to be dominant activities throughout the cold marine environment, indicating their importance in bacterial degradation of the organic matter. lip2 Gene from Psychrobacter sp. TA144, a micro-organism isolated from the Antarctic sea water, was cloned and over-expressed in Escherichia coli. The recombinant protein (PsyHSL) accumulated in the insoluble fraction from which it was recovered in active form, purified to homogeneity and deeply characterised. Temperature dependence of PsyHSL activity was typical of psychrophilic enzymes, with an optimal temperature of 35 °C at pH 8.0. The enzyme resulted to be active on pNP-esters of fatty acids with acyl chain length from C₂ to C₁₂ and the preferred substrate was pNP-pentanoate showing a k_cat = 26.2 ± 0.1 s⁻¹, K_M = 0.122 ± 0.006 mM and a k_cat/K_M = 215 ± 11 mM⁻¹ s⁻¹. The enzyme was strongly inhibited by Hg²⁺, Zn²⁺, Cu²⁺, Fe³⁺, Mn²⁺ ions and it resulted to be activated in presence of methanol and acetonitrile, with calculated C₅₀ values of 1.98 M and 0.92 M, respectively.     

Localized application of soil organic matter shifts distribution of cluster roots of white lupin in the soil profile due to localized release of phosphorus

Background and Aims

Phosphorus (P) is a major factor controlling cluster-root formation. Cluster-root proliferation tends to concentrate in organic matter (OM)-rich surface-soil layers, but the nature of this response of cluster-root formation to OM is not clear. Cluster-root proliferation in response to localized application of OM was characterized in Lupinus albus (white lupin) grown in stratified soil columns to test if the stimulating effect of OM on cluster-root formation was due to (a) P release from breakdown of OM; (b) a decrease in soil density; or (c) effects of micro-organisms other than releasing P from OM.

Methods

Lupin plants were grown in three-layer stratified soil columns where P was applied at 0 or 330 mg P kg⁻¹ to create a P-deficient or P-sufficient background, and OM, phytate mixed with OM, or perlite was applied to the top or middle layers with or without sterilization.

Key Results

Non-sterile OM stimulated cluster-root proliferation and root length, and this effect became greater when phytate was supplied in the presence of OM. Both sterile OM and perlite significantly decreased cluster-root formation in the localized layers. The OM position did not change the proportion of total cluster roots to total roots in dry biomass among no-P treatments, but more cluster roots were concentrated in the OM layers with a decreased proportion in other places.

Conclusions

Localized application of non-sterile OM or phytate plus OM stimulated cluster-root proliferation of L. albus in the localized layers. This effect is predominantly accounted for by P release from breakdown of OM or phytate, but not due to a change in soil density associated with OM. No evidence was found for effects of micro-organisms in OM other than those responsible for P release.     

Symbiosome-like intracellular colonization of cereals and other crop plants by nitrogen-fixing bacteria for reduced inputs of synthetic nitrogen fertilizers

It has been forecast that the challenge of meeting increased food demand and protecting environmental quality will be won or lost in maize, rice and wheat cropping systems, and that the problem of environmental nitrogen enrichment is most likely to be solved by substituting synthetic nitrogen fertilizers by the creation of cereal crops that are able to fix nitrogen symbiotically as legumes do. In legumes, rhizobia present intracellularly in membrane-bound vesicular compartments in the cytoplasm of nodule cells fix nitrogen endosymbiotically. Within these symbiosomes, membrane-bound vesicular compartments, rhizobia are supplied with energy derived from plant photosynthates and in return supply the plant with biologically fixed nitrogen, usually as ammonia. This minimizes or eliminates the need for inputs of synthetic nitrogen fertilizers. Recently we have demonstrated, using novel inoculation conditions with very low numbers of bacteria, that cells of root meristems of maize, rice, wheat and other major non-legume crops, such as oilseed rape and tomato, can be intracellularly colonized by the non-rhizobial, non-nodulating, nitrogen fixing bacterium, Gluconacetobacter diazotrophicus that naturally occurs in sugarcane. G. diazotrophicus expressing nitrogen fixing (nifH) genes is present in symbiosome-like compartments in the cytoplasm of cells of the root meristems of the target cereals and non-legume crop species, somewhat similar to the intracellular symbiosome colonization of legume nodule cells by rhizobia. To obtain an indication of the likelihood of adequate growth and yield, of maize for example, with reduced inputs of synthetic nitrogen fertilizers, we are currently determining the extent to which nitrogen fixation, as assessed using various methods, is correlated with the extent of systemic intracellular colonization by G. diazotrophicus, with minimal or zero inputs.     

Diverse fossil amoebae in German Mesozoic amber

Fossil amoebae are very rare, although their evolutionary history extends back into the Proterozoic. The Cenomanian amber of Schliersee (southern Germany) is very rich in micro-organisms and contains the highest diversity of fossil freshwater rhizopods (Gymnamoebia and Testacealobosia) yet discovered. Altogether seven testate amoebae and one gymnamoebian species are recorded from this Mesozoic amber. The four newly discovered taxa described in this paper can be assigned to the extant species Centropyxis delicatula , Centropyxis hirsuta , Phryganella acropodia and Phryganella paradoxa . Over 200 individuals of Phryganella paradoxa are preserved. Together with their syninclusions, the amoebae are species of limnetic or limnetic–terrestrial microcoenoses. The presence of 100-myr-old fossils with extant representatives suggests evolutionary stasis of these freshwater amoebae. However, not all modern testacean families have been recorded from Mesozoic limnetic habitats. Our experimental studies verify that naked and testate amoebae can be embedded in resins.     

Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and,with the exception of endosymbiotic gene transfers,few ancient transfer events persist

While there is compelling evidence for the impact of endosymbiotic gene transfer (EGT; transfer from either mitochondrion or chloroplast to the nucleus) on genome evolution in eukaryotes, the role of interdomain transfer from bacteria and/or archaea (i.e. prokaryotes) is less clear. Lateral gene transfers (LGTs) have been argued to be potential sources of phylogenetic information, particularly for reconstructing deep nodes that are difficult to recover with traditional phylogenetic methods. We sought to identify interdomain LGTs by using a phylogenomic pipeline that generated 13 465 single gene trees and included up to 487 eukaryotes, 303 bacteria and 118 archaea. Our goals include searching for LGTs that unite major eukaryotic clades, and describing the relative contributions of LGT and EGT across the eukaryotic tree of life. Given the difficulties in interpreting single gene trees that aim to capture the approximately 1.8 billion years of eukaryotic evolution, we focus on presence–absence data to identify interdomain transfer events. Specifically, we identify 1138 genes found only in prokaryotes and representatives of three or fewer major clades of eukaryotes (e.g. Amoebozoa, Archaeplastida, Excavata, Opisthokonta, SAR and orphan lineages). The majority of these genes have phylogenetic patterns that are consistent with recent interdomain LGTs and, with the notable exception of EGTs involving photosynthetic eukaryotes, we detect few ancient interdomain LGTs. These analyses suggest that LGTs have probably occurred throughout the history of eukaryotes, but that ancient events are not maintained unless they are associated with endosymbiotic gene transfer among photosynthetic lineages.     

Effects of microclimate on behavioural and life history traits of terrestrial isopods: implications for responses to climate change

The sensitivity of terrestrial isopods to changes in both temperature and moisture make them suitable models for examining possible responses of arthropod macro-decomposers to predicted climate change. Effects of changes in both temperature and relative humidity on aggregation, growth and survivorship of species of isopods contrasting in their morphological and physiological adaptations to moisture stress have been investigated in laboratory microcosms.All three traits were more sensitive to a reduction in relative humidity of 20–25% than they were to an increase in temperature of 5–6 °C. These results suggest that predicted changes in climate in south east England may reduce the extent to which soil animals stimulate microbial activity and hence carbon dioxide (CO₂) emissions from soils in the future. This may help to mitigate the potential for a positive feedback between increased CO₂ emissions from soils, and increased greenhouse effects causing an increase in soil temperatures.     

An assessment of vertical inheritance versus endosymbiont transfer of nucleus-encoded genes for mitochondrial proteins following tertiary endosymbiosis in Karlodinium micrum

Most photosynthetic dinoflagellates harbour a red alga-derived secondary plastid. In the dinoflagellate Karlodinium micrum, this plastid was replaced by a subsequent endosymbiosis, resulting in a tertiary plastid derived from a haptophyte. Evolution of endosymbionts entails substantial relocation of endosymbiont genes to the host nucleus: a process called endosymbiotic gene transfer (EGT). In K. micrum, numerous plastid genes from the haptophyte nucleus are found in the host nucleus, providing evidence for EGT in this system. In other cases of endosymbiosis, notably ancient primary endosymbiotic events, EGT has been inferred to contribute to remodeling of other cell functions by expression of proteins in compartments other than the endosymbiont from which they derived. K. micrum provides a more recently derived endosymbiotic system to test for evidence of EGT and gain of function in non-plastid compartments. In this study, we test for gain of haptophyte-derived proteins for mitochondrial function in K. micrum. Using molecular phylogenies we have analysed whether nucleus-encoded mitochondrial proteins were inherited by EGT from the haptophyte endosymbiont, or vertically inherited from the dinoflagellate host lineage. From this dataset we found no evidence of haptophyte-derived mitochondrial genes, and the only cases of non-vertical inheritance were genes derived from lateral gene transfer events.     

The microtubule analog protein, FtsZ, in the endosymbiont of trypanosomatid protozoa

Blastocrithidia culicis and Crithidia deanei are trypanosomatids that harbor an endosymbiotic bacterium in their cytoplasm. In prokaryotes, numerous proteins are essential for cell division, such as FtsZ, which is encoded by filament-forming temperature-sensitive (fts) genes. FtsZ is the prokaryotic homolog of eukaryotic tubulin and is present in bacteria and archaea, and has also been identified in mitochondria and chloroplasts. FtsZ plays a key role in the initiation of cytokinesis. It self-assembles into the Z ring, which establishes the division plane during septation. In this study, immunoblotting analysis using a FtsZ polyclonal antibody, revealed a 40-kDa band characteristic of FtsZ in endosymbiont fractions and in whole trypanosomatid homogenates, but not in whole cell extracts of aposymbiotic strains. Confocal microscopy and ultrastructural analysis revealed a specific and dispersed labeling over the endosymbiont. Bars and ring-like structures, which are suggestive of the presence of Z-rings, were never observed, even during the division of the symbiont. This peculiar distribution of FtsZ may represent an arrangement of cytoskeleton protein intermediate between prokaryotic and eukaryotic cells. The endosymbiont ftsz gene was completely sequenced after amplification of DNA from symbiont-bearing trypanosomatids or from pure endosymbiont fractions, using PCR and specific primers. The sequences obtained from the endosymbionts from C. deanei and B. culicis were very similar, and were most closely related to bacteria from the genus Pseudomonas.