Diversity among bacteria isolated from the deep subsurface

Culturable bacteria from the deep subsurface (179 m) at Cerro Negro, New Mexico were isolated and characterized. The average number of viable aerobic bacteria was estimated to be 5×10⁵g^–1 of sediment, but only about 0.1% of these could be recovered on agar medium when incubated under aerobic conditions. Of 158 strains isolated from this depth, 92 were characterized by cellular fatty acid profiles (FAME), 36 by analysis of partial 16S rDNA sequences, and 44 by rep-PCR genome fingerprint analysis using three different sets of oligonucleotide primers (REP, BOX, or ERIC). These analyses showed the majority of isolates (67%) were Gram-positive bacteria and primarily members of genera with a high %G+C DNA. The remaining isolates were -subdivisionProteobacteria (19%) and members of the flavobacteria group (14%). The diversity indices based on these different methods of characterization were very high suggesting this subsurface habitat harbors a highly diverse microbial community.     

Surface layer proteins in species of the family Lactobacillaceae

The S-layer or surface layer protein (SLP) is the most ancient biological envelope, highly conserved in several Bacteria and Archaea. In lactic acid bacteria (LAB), SLP is only found in species belonging to the Lactobacillaceae family, many of them considered probiotic microorganisms. New reclassification of members within the Lactobacillaceae family (International Journal of Systematic and Evolutionary Microbiology, 2020, 70 , 2782) and newly sequenced genomes demands an updated revision on SLP genes and domain organization. There is growing information concerning SLP occurrence, molecular biology, biophysical properties, and applications. Here, we focus on the prediction of slp genes within the Lactobacillaceae family, and specifically, on the neat interconnection between the two different modular SLP domain organizations and the new reclassified genera. We summarize the results in a concise tabulated manner to review the present knowledge on SLPs and discuss the most relevant and updated concepts regarding SLP sequence clustering. Our assessment is based on sequence alignments considering the new genera classification and protein domain definition with post-translational modifications. We analyse the difficulties encountered to resolve the SLPs 3D structure, describing the need for structure prediction approaches and the relation between protein structure and its anchorage mechanism to the cell wall. Finally, we enumerate new SLP applications regarding heterologous display, pathogen exclusion, immunostimulation, and metal binding.     

Phylogenetic reconstruction of the Drosophila obscura group, on the basis of mitochondrial DNA

We have constructed restriction-site maps of the mtDNAs in 13 species and one subspecies of the Drosophila obscura group. The traditional division of this group into two subgroups (affinis and obscura) does not correspond to the phylogeny of the group, which shows two well- defined clusters (the Nearctic affinis and pseudoobscura subgroups) plus a very heterogeneous set of anciently diverged species (the Palearctic obscura subgroup). The mtDNA of Drosophila exhibits a tendency to evolve toward high A+T values. This leads to a "saturation" effect that (1) begets an apparent decrease in the rate of evolution as the time since the divergence of taxa increases and (2) reduces the value that mtDNA restriction analysis has for the phylogenetic reconstruction of Drosophila species that are not closely related.      

Customizing CO<Subscript>2</Subscript> allocation using a new non-iterative method to reflect operational constraints in complex EU refineries

Purpose

Developing a robust method for CO₂ allocation in oil refineries is an ongoing debate within the life cycle assessment (LCA) community. Several methodologies reported in the literature, mostly performing sequential and iterative calculations, tend to be biased toward diesel at the expense of gasoline, failing to properly consider the role played by hydrogen. This paper develops a new non-iterative refinery CO₂ allocation method to explore the concept of customized allocation to overcome the inherent bias in standard methods.

Methods

The allocation methodology is based on a system of linear equations built around the material and energy balances of a refinery. After describing the process of building such system, it is shown that the carbon allocation values of all final products and intermediate streams are directly obtained by solving it. A numerical example of CO₂ emission allocation to major refinery products is provided from an optimized refinery linear programming (LP) case for the European refining industry, based on literature projections for 2020.

Results and discussion

The paper presents the key emission sources in the European refinery sector, and by using a standard mass-based allocation technique, we show that the carbon intensities of refined petroleum products derived using the non-iterative method are consistent with other studies. We confirm the findings that the standard allocation typically used in attributional refinery LCA tends to reward diesel to the detriment of gasoline. We attempted reconciling this by applying a reallocation factor to customize the CO₂ allocation to represent the “real” economic purposes of process units reflecting the constraints European refineries face today. This moderated the octane production effects given the important role the reformer plays in hydrogen co-production, where the emission burden of highly knock-resistant reformate is redistributed to hydrogen and carried through to diesel.

Conclusions

By customizing the allocation of CO₂, we demonstrated that the differences between a consequential and an attributional approach in refinery LCA can partly be reconciled. We now run into the risk of increasing the subjectivity of the attributional method by using “judgment calls” to decide on the choice of weightage to be applied. We invite the wider LCA practitioners to further investigate the use of this new non-iterative method for allocating CO₂ and explore the concept of reallocation factors as means to customize emission allocation.

     

Myrothecium-like (Ascomycota,Hypocreales) species from tropical areas: <Emphasis Type="Italic">Digitiseta</Emphasis> gen. nov. and additions to <Emphasis Type="Italic">Inaequalispora</Emphasis> and <Emphasis Type="Italic">Parvothecium</Emphasis>

Inaequalispora and Parvothecium are two myrothecium-like, closely related genera of Hypocreales. They are also morphologically similar, sharing sporodochial conidiomata, penicillate conidiophores, fusiform to ellipsoidal conidia accumulating in a green slimy drop, and hypha-like setoid extensions emerging through the conidial mass. During a revision of myrothecium-like isolates originating from rainforest areas of South America (Ecuador, Brazil) and Southeast Asia (Singapore), multilocus phylogenetic inferences (based on DNA sequence data of ITS, partial nuc 28S, and partial tef1a, rpb2 and tub2) and morphological studies concordantly revealed the occurrence of two undescribed species of Inaequalispora (I. longiseta sp. nov. and I. cylindrospora sp. nov.) and one undescribed species of Parvothecium (P. amazonensesp. nov.). Myrothecium setiramosum, M. dimorphum, and two undescribed taxa form the base of a new lineage, sister to the current Parvothecium lineage. This lineage is recognized as Digitiseta gen. nov., typified by D. setiramosa comb. nov. Digitiseta dimorpha comb. nov. is also proposed, and the new species D. parvodigitata sp. nov. and D. multidigitata sp. nov. are described.     

Intracellular calcium buffering capacity in isolated squid axons

Changes in ionized calcium were studied in axons isolated from living squid by measuring absorbance of the Ca binding dye Arsenazo III using multiwavelength differential absorption spectroscopy. Absorption changes measured in situ were calibrated in vitro with media of ionic composition similar to axoplasm containing CaEGTA buffers. Calcium loads of 50-2,500 μmol/kg axoplasm were induced by microinjection, by stimulation in 112 mM Ca seawater, or by soaking in choline saline with 1-10 mM Ca. Over this range of calcium loading of intact axoplasm, the ionized calcium in the axoplasm rose about 0.6 nM/μM load. Similar loading in axons preteated with carbonyl cyanide 4- trifluoromethoxyphenylhydrazone (FCCP) to inhibit the mitochondrial proton gradient increased ionized calcium by 5-7 percent of the imposed load, i.e. 93-95 percent of the calcium load was buffered by a process insensitive to FCCP. This FCCP- insensitive buffer system was not saturated by the largest calcium loads imposed, indicating a capacity of at least several millimolar. Treatment of previously loaded axons with FCCP or apyrase plus cyanide produced rises in ionized calcium which could be correlated with the extent of the load. Analysis of results indicated that, whereas only 6 percent of the endogenous calcium in fresh axons is stored in the FCCP-sensitive (presumably mitochondrial) buffer system, about 30 percent of an imposed exogenous load in the range of 50-2,500 μM is taken up by this system.     

Effects of different levels of CO2 on photosynthesis and cell components of the red alga Porphyra leucosticta

Photosynthesis and cell composition of Porphyraleucosticta discs grown at low (< 0.0001% in air), current (control) and high (1% CO₂ in air)inorganic carbon (C_i) concentrations were analyzed. Carbohydrate content in discs grown at high C_i increased (15.1 mg g^-1 FW) with respect to the control (6.4 mg g FW^-1), whereas soluble protein content decreased to one-third (5.6 to2.1 mg g^-1 FW). Carbohydrate content was unaffected and soluble protein slightly increased in discs grown at low C_i. As a consequence of these changes, a lower C/N molar ratio (8.6) was found in the discs grown at low compared to high C_i(12.4). Nitrate reductase activity increased at high C_i from 0.3 ± 0.2 to 1.7 ± 0.4 μmolNO₂ ^- g^-1 FW h^-1indicating that reduction and assimilation of nitrate were uncoupled. The response of photosynthesis to increasing irradiance, estimated from O₂evolution vs. irradiance curves, was affected by the treatments. Maximum quantum yield (Φ _O2°) and effective quantum yield (Φ _O2) at 150 μmol photon m^-2s^-1 decreased by 20% and 50%, respectively, at low C_i. These differences could be due to changes in photosynthetic electron flow between PSII and PSI. Treatments also produced changes in maximal (F_v/F_m) and effective (ΔF/F_m′)quantum yield for photosystem II charge separation. This revised version was published online in August 2006 with corrections to the Cover Date.     

Nitrate Reductase Activity in an Eutrophic Reservoir duringthe Stratification Cycle

Nitrate reductase activity was measured during the stratification cycle of the eutrophic reservoir La Concepción. Nitrate was consumed in the epilimnion mainly through assimilatory reduction, and in the hypolimnion through dissimilatory reduction triggered by anoxic conditions. Nitrate reductase activity (NR) scaled to particulate nitrogen (PN) was positively correlated with the external nitrate concentration and the NO₃^–/NH₄⁺ ratio. Using NR as a tool for the assessment of the N cycle dynamics, it can be suggested that at the beginning of the stratification cycle, the phytoplanktonic community was mainly using NO₃^– as N source; and since N was not likely the limiting nutrient at that time of the year, NR was close to its maximum possible.     

Establishing the South Australian Macrobenthic Traits (SAMT) database: A trait classification for functional assessments

Trait‐based approaches are increasingly used as a proxy for understanding the relationship between biodiversity and ecosystem functioning. Macrobenthic fauna are considered one of the major providers of ecosystem functions in marine soft sediments; however, several gaps persist in the knowledge of their trait classification, limiting the potential use of functional assessments. While trait databases are available for the well‐studied North Atlantic benthic fauna, no such trait classification system exists for Australia. Here, we present the South Australian Macrobenthic Traits (SAMT) database, the first comprehensive assessment of macrobenthic fauna traits in temperate Australian waters. The SAMT database includes 13 traits and 54 trait‐modalities (e.g., life history, morphology, physiology, and behavior), and is based on records of macrobenthic fauna from South Australia. We provide trait information for more than 250 macrobenthic taxa, including outcomes from a fuzzy coding procedure, as well as an R package for using and analyzing the SAMT database. The establishment of the SAMT constitutes the foundation for a comprehensive macrobenthic trait database for the wider southern Australian region that could facilitate future research on functional perspectives, such as assessments of functional diversity and changes to ecosystem functioning.