Microbial communities in large-scale wood piles and their effects on wood quality and the environment

The demand of renewable energy sources, i.e. biomass, is steadily increasing worldwide to reduce the need of fossil energy sources. Biomass such as energy crops, woody species, forestry and agricultural residues are the most common renewable energy sources. Due to uneven demand for wood fuel, the material is mostly stored outdoors in chip piles or as logs until utilisation. Storage of biomass is accompanied by chemical, physical and biological processes which can significantly reduce the fuel quality. However, heating plants require high-quality biomass to ensure efficient operation, thereby minimising maintenance costs. Therefore, optimised storage conditions and duration times for chipped wood and tree logs have to be found. This paper aims at reviewing available knowledge on the pathways of microbial effects on stored woody biomass and on investigations of the fungal and bacterial community structure and identity. Moreover, potential functions of microorganisms present in wood chip piles and logs are discussed in terms of (1) reduction of fuel quality, (2) catalysing self-ignition processes, and (3) constituting health risk and unfriendly work environment.     

Elevated poly(3-hydroxybutyrate) synthesis in mutants of Ralstonia eutropha H16 defective in lipopolysaccharide biosynthesis

Several independent transposon Tn5-induced mutants of Ralstonia eutropha H16 exhibited a poly(3-hydroxybutyric acid) (PHB) elevated phenotype and accumulated substantial amounts of PHB already in the exponential growth phase. The insertion loci of Tn5 in these six mutants were mapped in the genes hldA (twice), hldC (twice), rfaF2, and rfaF3, which are all involved in the synthesis of lipopolysaccharides (LPS), an important component of the outer membrane (OM) of Gram-negative bacteria. The generated defined deletion mutant ΔhldA confirmed the PHB elevated phenotype. According to the literature,such a truncated LPS may cause an increased permeability of the OM; thereby, the mutations may lead to a facilitated uptake of carbon source from the medium as exemplarily shown for gluconate and succinate. Thus, the ratio of carbon to nitrogen in the cell is increased. Proteome analyses revealed reinforcement of the Entner–Doudoroff pathway and of subsequent reactions that finally may lead to higher concentrations of acetyl-CoA in the cells. Due to the impaired synthesis of complete LPS, intermediates of LPS biosynthesis might be recycled by reactions yielding higher levels of NADPH and acetyl-CoA. Since the latter are precursors for synthesis of PHB, this could explain the elevated synthesis and accumulation of this polymer in case of the LPS mutants.     

Insights into ubiquitin-conjugating enzyme/ co-activator interactions from the structure of the Pex4p:Pex22p complex

Ubiquitin-conjugating enzymes (E2s) coordinate distinct types of ubiquitination via specific E3 ligases, to a large number of protein substrates. While many E2 enzymes need only the presence of an E3 ligase for substrate ubiquitination, a number of E2s require additional, non-canonical binding partners to specify their function. Here, we have determined the crystal structure and function of an E2/co-activator assembly, the Pex4p:Pex22p complex. The peroxisome-associated E2 enzyme Pex4p binds the peroxisomal membrane protein Pex22p through a binding site that does not overlap with any other known interaction interface in E2 enzymes. Pex22p association enhances Pex4p's ability to transfer ubiquitin to a substrate in vitro, and Pex22p binding-deficient forms of Pex4p are unable to ubiquitinate the peroxisomal import receptor Pex5p in vivo. Our data demonstrate that the Pex4p:Pex22p assembly, and not Pex4p alone, functions as the E2 enzyme required for Pex5p ubiquitination, establishing a novel mechanism of E2 enzyme regulation.     

A new class of carriers that transport selective cargo from the trans Golgi network to the cell surface

We have isolated a membrane fraction enriched in a class of transport carriers that form at the trans Golgi network (TGN) and are destined for the cell surface in HeLa cells. Protein kinase D (PKD) is required for the biogenesis of these carriers that contain myosin II, Rab6a, Rab8a, and synaptotagmin II, as well as a number of secretory and plasma membrane‐specific cargoes. Our findings reveal a requirement for myosin II in the migration of these transport carriers but not in their biogenesis per se. Based on the cargo secreted by these carriers we have named them CARTS for CAR riers of the T GN to the cell S urface. Surprisingly, CARTS are distinct from the carriers that transport vesicular stomatitis virus (VSV)‐G protein and collagen I from the TGN to the cell surface. Altogether, the identification of CARTS provides a valuable means to understand TGN to cell surface traffic.     

A nomenclature for intestinal in vitro cultures

Many advances have been reported in the long-term culture of intestinal mucosal cells in recent years. A significant number of publications have described new culture media, cell formations, and growth patterns. Furthermore, it is now possible to study, e.g., the capabilities of isolated stem cells or the interactions between stem cells and mesenchyme. However, at the moment there is significant variation in the way these structures are described and named. A standardized nomenclature would benefit the ability to communicate and compare findings from different laboratories using the different culture systems. To address this issue, members of the NIH Intestinal Stem Cell Consortium herein propose a systematic nomenclature for in vitro cultures of the small and large intestine. We begin by describing the structures that are generated by preparative steps. We then define and describe structures produced in vitro, specifically: enterosphere, enteroid, reconstituted intestinal organoid, induced intestinal organoid, colonosphere, colonoid, and colonic organoid.     

The unfolding story of a redox chaperone

Oxidative stress, especially in combination with heat stress, poses a life-threatening challenge to many organisms by causing protein misfolding and aggregation. In this issue, Reichmann et al. demonstrate how a destabilized linker region of the bacterial chaperone Hsp33 prevents aggregation of a denatured protein by stabilizing structural elements.     

Chemotaxis of Marinobacter adhaerens and Its Impact on Attachment to the Diatom Thalassiosira weissflogii

Alga-bacterium interactions are crucial for aggregate formation and carbon cycling in aquatic systems. To understand the initiation of these interactions, we investigated bacterial chemotaxis within a bilateral model system. Marinobacter adhaerens HP15 has been demonstrated to attach to the diatom Thalassiosira weissflogii and induce transparent exopolymeric particle and aggregate formation. M. adhaerens possesses one polar flagellum and is highly motile. Bacterial cells were attracted to diatom cells, as demonstrated by addition of diatom cell homogenate or diatom culture supernatant to soft agar, suggesting that chemotaxis might be important for the interaction of M. adhaerens with diatoms. Three distinct chemotaxis-associated gene clusters were identified in the genome sequence of M. adhaerens, with the clusters showing significant sequence similarities to those of Pseudomonas aeruginosa PAO1. Mutations in the genes cheA, cheB, chpA, and chpB, which encode histidine kinases and methylesterases and which are putatively involved in either flagellum-associated chemotaxis or pilus-mediated twitching motility, were generated and mutants with the mutations were phenotypically analyzed. ΔcheA and ΔcheB mutants were found to be swimming deficient, and all four mutants were impaired in biofilm formation on abiotic surfaces. Comparison of the HP15 wild type and its chemotaxis mutants in cocultures with the diatom revealed that the fraction of bacteria attaching to the diatom decreased significantly for mutants in comparison to that for the wild type. Our results highlight the importance of M. adhaerens chemotaxis in initiation of its interaction with the diatom. In-depth knowledge of these basic processes in interspecies interactions is pivotal to obtain a systematic understanding of organic matter flux and nutrient cycling in marine ecosystems.     

Selected coccal green algae are not affected by the humic substance Huminfeed<Superscript>®</Superscript> in term of growth or photosynthetic performance

Humic substances (HSs) have been shown to influence growth, photophysiology, and redox homeostasis in phototrophs. However, many ecological studies deliver controversial results indicating inhibitory or stimulating effects depending on the kind of phototrophic organism or type of HSs applied. Here we analyzed the effect of Huminfeed^® (HF), a preparation from leonardite associated with lignite deposits, on growth and photosynthetic performance of three different coccal green algae. Concentrations of HF in the range of 2–20 mg l^?1 dissolved organic carbon (DOC) did neither affect the growth rate nor the light-adapted photosynthetic electron transport. Even photoinhibitory light intensities of 1,600 μmol photons m^?2 s^?1, representing the tenfold of growth light intensity, did not result in a decline of the maximal photosynthetic rate in HF-treated algae. In HF-grown algae, a very subtle decrease by about 10% could be observed in thermoluminescent light emission, a sensitive method to detect changes in photosystem II (PSII) chemistry. However, thermoluminescence (TL) represents only 3% of the light-induced charge separated states in PSII. Hence, rather small changes will not have significant effects on overall photosynthetic performance and growth. Therefore, the physiological effect of HSs on freshwater phototrophs has to be revisited.