Are diatom diversity indices reliable monitoring metrics?

A biological survey was carried out in 640 stations spread over the Loire-Bretagne National Network (France) between 1996 and 2000. Epilithic diatom inventories were obtained following standard methods. A total of 934 diatom taxa were identified. Common diversity indices (species richness, Shannon’s diversity, equitability, dominance, etc.) were calculated and compared against abiotic factors verify their reliability as biomonitoring metrics. Sampling stations were classified according to their trophic status (TP concentration). Several theoretical predictions about the relationship between community structural parameters and limnological variables were tested. In general, diversity indices exhibited poor linear correlations with environmental factors indicating ecological status. No clear patterns were found concerning species accumulation curves, occurrence-abundance, frequency-abundance and frequency distribution of diatom taxa between different trophic levels, although assemblages from stations with lower TP levels were characterized by relatively high dominances of certain taxa, mainly Achnanthidium minutissimum. In the light of these findings, the use of diatom diversity indices in biological quality surveillance protocols in continental waters is discouraged. Results are compared and discussed with similar studies.     

Effect of streamlining taxa lists on diatom-based indices: implications for intercalibrating ecological status

Intercalibration of ecological status class boundaries between member states is a requirement of the European Union’s Water Framework Directive. Although a preliminary intercalibration of boundaries established for phytobenthos has been performed, a number of questions remain, including the extent to which variations in taxonomic concepts used in different member states influences the position of these boundaries. In this paper, the robustness of the diatom-based metrics used for intercalibration is assessed. Whilst use of genus-level identification led to a loss of ecological information, merging representatives of closely-related taxa has little effect on these metrics. Similarly, taxa that occur only rarely or never have high relative abundances in a dataset can also be ignored without the loss of ecological information. Similar results were obtained when modern taxonomic concepts were compared with concepts in use 80 years ago. Fine scale taxonomy may play a valuable role within member states; however, our results suggest that, at a continental scale, a simplified approach to diatom taxonomy should not affect intercalibration results.     

Ecological assessment of Portuguese reservoirs based on littoral epilithic diatoms

Hydrobiologia - The objective of this study was to evaluate whether biological methods based on epilithic littoral diatoms are a valuable complement to other biological elements for the assessment...     

Genome sequence of Fibrella aestuarina BUZ 2(T), a filamentous marine bacterium

Fibrella aestuarina BUZ 2(T) is the type strain of the recently characterized genus Fibrella. Here we report the draft genome sequence of this strain, which consists of a single scaffold representing the chromosome (with 11 gaps) and a 161-kb circular plasmid.     

Chromosomal replication initiation machinery of low-g+c-content firmicutes

Much of our knowledge of the initiation of DNA replication comes from studies in the Gram-negative model organism Escherichia coli. However, the location and structure of the origin of replication within the E. coli genome and the identification and study of the proteins which constitute the E. coli initiation complex suggest that it might not be as universal as once thought. The archetypal low-G+C-content Gram-positive Firmicutes initiate DNA replication via a unique primosomal machinery, quite distinct from that seen in E. coli, and an examination of oriC in the Firmicutes species Bacillus subtilis indicates that it might provide a better model for the ancestral bacterial origin of replication. Therefore, the study of replication initiation in organisms other than E. coli, such as B. subtilis, will greatly advance our knowledge and understanding of these processes as a whole. In this minireview, we highlight the structure-function relationships of the Firmicutes primosomal proteins, discuss the significance of their oriC architecture, and present a model for replication initiation at oriC.     

Determination of Ligand Pathways in Globins: APOLAR TUNNELS VERSUS POLAR GATES*

Although molecular dynamics simulations suggest multiple interior pathways for O₂ entry into and exit from globins, most experiments indicate well defined single pathways. In 2001, we highlighted the effects of large-to-small amino acid replacements on rates for ligand entry and exit onto the three-dimensional structure of sperm whale myoglobin. The resultant map argued strongly for ligand movement through a short channel from the heme iron to solvent that is gated by the distal histidine (His-64(E7)) near the solvent edge of the porphyrin ring. In this work, we have applied the same mutagenesis mapping strategy to the neuronal mini-hemoglobin from Cerebratulus lacteus (CerHb), which has a large internal tunnel from the heme iron to the C-terminal ends of the E and H helices, a direction that is 180° opposite to the E7 channel. Detailed comparisons of the new CerHb map with expanded results for Mb show unambiguously that the dominant (>90%) ligand pathway in CerHb is through the internal tunnel, and the major (>75%) ligand pathway in Mb is through the E7 gate. These results demonstrate that: 1) mutagenesis mapping can identify internal pathways when they exist; 2) molecular dynamics simulations need to be refined to address discrepancies with experimental observations; and 3) alternative pathways have evolved in globins to meet specific physiological demands.     

Lipin-2 reduces proinflammatory signaling induced by saturated fatty acids in macrophages

Lipin-2 is a member of the lipin family of enzymes, which are key effectors in the biosynthesis of lipids. Mutations in the human lipin-2 gene are associated with inflammatory-based disorders; however, the role of lipin-2 in cells of the immune system remains obscure. In this study, we have investigated the role of lipin-2 in the proinflammatory action of saturated fatty acids in murine and human macrophages. Depletion of lipin-2 promotes the increased expression of the proinflammatory genes Il6, Ccl2, and Tnfα, which depends on the overstimulation of the JNK1/c-Jun pathway by saturated fatty acids. In contrast, overexpression of lipin-2 reduces the release of proinflammatory factors. Metabolically, the absence of lipin-2 reduces the cellular content of triacylglycerol in saturated fatty acid-overloaded macrophages. Collectively, these studies demonstrate a protective role for lipin-2 in proinflammatory signaling mediated by saturated fatty acids that occurs concomitant with an enhanced cellular capacity for triacylglycerol synthesis. The data provide new insights into the role of lipin-2 in human and murine macrophage biology and may open new avenues for controlling the fatty acid-related low grade inflammation that constitutes the sine qua non of obesity and associated metabolic disorders.     

Conservation agriculture, increased organic carbon in the top-soil macro-aggregates and reduced soil CO2 emissions

Background and aims

Conservation agriculture, the combination of minimal soil movement (zero or reduced tillage), crop residue retention and crop rotation, might have the potential to increase soil organic C content and reduce emissions of CO₂.

Methods

Three management factors were analyzed: (1) tillage (zero tillage (ZT) or conventional tillage (CT)), (2) crop rotation (wheat monoculture (W), maize monoculture (M) and maize-wheat rotation (R)), and (3) residue management (with (+r), or without (?r) crop residues). Samples were taken from the 0–5 and 5–10?cm soil layers and separated in micro-aggregates (< 0.25?mm), small macro-aggregates (0.25 to 1?mm) and large macro-aggregates (1 to 8?mm). The carbon content of each aggregate fraction was determined.

Results

Zero tillage combined with crop rotation and crop residues retention resulted in a higher proportion of macro-aggregates. In the 0–5?cm layer, plots with a crop rotation and monoculture of maize and wheat in ZT+r had the greatest proportion of large stable macro-aggregates (40%) and highest mean weighted diameter (MWD) (1.7?mm). The plots with CT had the largest proportion of micro-aggregates (27%). In the 5–10?cm layer, plots with residue retention in both CT and ZT (maize 1?mm and wheat 1.5?mm) or with monoculture of wheat in plots under ZT without residues (1.4?mm) had the greatest MWD. The 0–10?cm soil layer had a greater proportion of small macroaggregates compared to large macro-aggregates and micro-aggregates. In the 0–10?cm layer of soil with residues retention and maize or wheat, the greatest C content was found in the small and large macro-aggregates. The small macro-aggregates contributed most C to the organic C of the sample. For soil cultivated with maize, the CT treatments had significantly higher CO₂ emissions than the ZT treatments. For soil cultivated with wheat, CTR-r had significantly higher CO₂ emissions than all other treatments.

Conclusion

Reduction in soil disturbance combined with residue retention increased the C retained in the small and large macro-aggregates of the top soil due to greater aggregate stability and reduced the emissions of CO₂ compared with conventional tillage without residues retention and maize monoculture (a cultivation system normally used in the central highlands of Mexico).     

Four decades of post-agricultural forest development have caused major redistributions of soil phosphorus fractions

Fertilisation of agricultural land causes an accumulation of nutrients in the top soil layer, among which phosphorus (P) is particularly persistent. Changing land use from farmland to forest affects soil properties, but changes in P pools have rarely been studied despite their importance to forest ecosystem development. Here, we describe the redistributions of the P pools in a four-decadal chronosequence of post-agricultural common oak (Quercus robur L.) forests in Belgium and Denmark. The aim was to assess whether forest age causes a repartitioning of P throughout the various soil P pools (labile P, slowly cycling P and occluded P); in particular, we addressed the time-related alterations in the inorganic versus organic P fractions. In less than 40 years of oak forest development, significant redistributions have occurred between different P fractions. While both the labile and the slowly cycling inorganic P fractions significantly decreased with forest age, the organic fractions significantly increased. The labile P pool (inorganic + organic), which is considered to be the pool of P most likely to contribute to plant-available P, significantly decreased with forest age (from >20 to <10% of total P), except in the 0-5 cm of topsoil, where labile P remained persistently high. The shift from inorganic to organic P and the shifts between the different inorganic P fractions are driven by biological processes and also by physicochemical changes related to forest development. It is concluded that the organic labile P fraction, which is readily mineralisable, should be taken into account when studying the bioavailable P pool in forest ecosystems.