Comparative phylogenetic analyses of Halomonas variabilis and related organisms based on 16S rRNA, gyrB and ectBC gene sequences

Halomonas variabilis and phylogenetically related organisms were isolated from various habitats such as Antarctic terrain and saline ponds, deep-sea sediment, deep-sea waters affected by hydrothermal plumes, and hydrothermal vent fluids. Ten strains were selected for physiological and phylogenetic characterization in detail. All of those strains were found to be piezotolerant and psychrotolerant, as well as euryhaline halophilic or halotolerant. Their stress tolerance may facilitate their wide occurrence, even in so-called extreme environments. The 16S rDNA-based phylogenetic relationship was complemented by analyses of the DNA gyrase subunit B gene (gyrB) and genes involved in the synthesis of the major compatible solute, ectoine: diaminobutyric acid aminotransferase gene (ectB) and ectoine synthase gene (ectC). The phylogenetic relationships of H. variabilis and related organisms were very similar in terms of 16S rDNA, gyrB, and ectB. The ectC-based tree was inconsistent with the other phylogenetic trees. For that reason, ectC was inferred to derive from horizontal transfer.     

Aggregate Size and Architecture Determine Microbial Activity Balance for One-Stage Partial Nitritation and Anammox

Aerobic ammonium-oxidizing bacteria (AerAOB) and anoxic ammonium-oxidizing bacteria (AnAOB) cooperate in partial nitritation/anammox systems to remove ammonium from wastewater. In this process, large granular microbial aggregates enhance the performance, but little is known about granulation so far. In this study, three suspended-growth oxygen-limited autotrophic nitrification-denitrification (OLAND) reactors with different inoculation and operation (mixing and aeration) conditions, designated reactors A, B, and C, were used. The test objectives were (i) to quantify the AerAOB and AnAOB abundance and the activity balance for the different aggregate sizes and (ii) to relate aggregate morphology, size distribution, and architecture putatively to the inoculation and operation of the three reactors. A nitrite accumulation rate ratio (NARR) was defined as the net aerobic nitrite production rate divided by the anoxic nitrite consumption rate. The smallest reactor A, B, and C aggregates were nitrite sources (NARR, >1.7). Large reactor A and C aggregates were granules capable of autonomous nitrogen removal (NARR, 0.6 to 1.1) with internal AnAOB zones surrounded by an AerAOB rim. Around 50% of the autotrophic space in these granules consisted of AerAOB- and AnAOB-specific extracellular polymeric substances. Large reactor B aggregates were thin film-like nitrite sinks (NARR, <0.5) in which AnAOB were not shielded by an AerAOB layer. Voids and channels occupied 13 to 17% of the anoxic zone of AnAOB-rich aggregates (reactors B and C). The hypothesized granulation pathways include granule replication by division and budding and are driven by growth and/or decay based on species-specific physiology and by hydrodynamic shear and mixing.In the last few years, autotrophic nitrogen removal via partial nitritation and anoxic ammonium oxidation (anammox) has evolved from lab- to full-scale treatment of nitrogenous wastewaters with a low biodegradable organic compound content, and this evolution has been driven mainly by a significant decrease in the operational costs compared to the costs of conventional nitrification and heterotrophic denitrification (11, 23). Oxygen-limited autotrophic nitrification and denitrification (OLAND) is one of the autotrophic processes used and is a one-stage procedure; i.e., partial nitritation and anammox occur in the same reactor (30). The “functional” autotrophic microorganisms in OLAND include aerobic ammonium-oxidizing bacteria (AerAOB) and anoxic ammonium-oxidizing bacteria (AnAOB). With oxygen, AerAOB oxidize ammonium to nitrite (nitritation), and with the nitrite AnAOB oxidize the residual ammonium to form dinitrogen gas and some nitrate (anammox). Additional aerobic nitrite oxidation to nitrate (nitratation) by nitrite-oxidizing bacteria (NOB) lowers the nitrogen removal efficiency, but it can, for instance, be prevented at low dissolved oxygen (DO) levels because the oxygen affinity of AerAOB is higher than that of NOB (16). Reactor configurations for the OLAND process can be based on suspended biomass growing in aggregates, like that in a sequencing batch reactor (SBR) (37) or a gas lift or upflow reactor (32). For suspended-growth systems there are two important challenges: biomass retention and equilibrated microbial activities.High biomass retention efficiency is a prerequisite in anammox technologies because of the slow growth of AnAOB (33). In suspended biomass systems, settling properties determine the retention of biomass and are related to the microbial aggregate morphology (floc or granule) and size. Granules can be defined as compact and dense aggregates with an approximately spherical external appearance that do not coagulate under decreased hydrodynamic shear conditions and settle significantly faster than flocs (18). Toh and coworkers calculated a lower sludge volume index for aerobic granules than for aerobic flocs and also showed that there was an increase in the settling velocity with increasing granule size (35). Hence, in terms of physical properties, large granules are preferable for suspended-growth applications.OLAND aggregate size not only influences settling properties but also affects the proportion of microbial nitrite production and consumption; lower AerAOB activity and higher AnAOB activity were observed with larger aggregates (25, 37). Theoretically, a microbial aggregate with equal nitrite production and nitrite consumption can remove ammonium autonomously, because of its independence from other aggregates for acquisition and conversion of nitrite. Hence, with an increasing aggregate size and thus with a decreasing ratio of nitrite production to nitrite consumption, three functional categories of aggregates can be distinguished: nitrite sources, autonomous nitrogen removers, and nitrite sinks. Because minimal nitrite accumulation is one of the prerequisites for high nitrogen removal efficiency in OLAND reactors, the presence of excess small aggregates is undesirable (9, 37).Although large granular aggregates are desirable for biomass retention and activity balance, so far no formation mechanisms have been proposed for OLAND granules, in contrast to the well-studied anaerobic (13) and aerobic (1) granules. In order to determine general and environment-specific determinants for aggregate size and architecture, three suspended-growth OLAND reactors with different inoculation and operation (mixing and aeration) parameters were selected, and these reactors were designated reactors A, B, and C (Table ​(Table1).1). The first objective of this study was to gain more insight into the relationship between OLAND aggregate size, AerAOB and AnAOB abundance, and the activity balance. The second objective was to propose pathways for aggregation and granulation by relating (dis)similarities in aggregate size distribution, morphology, and architecture to differences in reactor inoculation and operation.

TABLE 1.

Overview of the three OLAND reactor systems from which suspended biomass samples were obtained

Multi-male group and bidirectional sex change in the gobiid fish, <Emphasis Type="Italic">Trimma caudomaculatum</Emphasis>

The gobiid fish, Trimma caudomaculatum, lives in groups. We investigated group structure, mating system and bidirectional sex change of this species. Four groups examined contained more than two males. The males were significantly larger than the females. By the observations in aquarium, the males occupied a nest and the females visited the nest for spawning. While there was no specific pair bond, the males mated with multiple females. Hence, this species establishes multi-male groups. In the experiments, four larger females had changed sex to male among 25 females. The smallest male changed to female in the group of four males.     

Phospholipase D from Streptoverticillium cinnamoneum: protein engineering and application for phospholipid production

This review is focusing on an industrially important enzyme, phospholipase D (PLD), exhibiting both transphosphatidylation and hydrolytic activities for various phospholipids. The transphosphatidylation activity of PLD is particularly useful for converting phosphatidylcholine (PC) into other phospholipids. During the last decade, the genes coding for PLD have been identified from various species including mammals, plants, yeast, and bacteria. However, detailed basic and applied enzymological studies on PLD have been hampered by the low productivity in these organisms. Efficient production of a recombinant PLD has also been unsuccessful so far. We recently isolated and characterized the PLD gene from Streptoverticillium cinnamoneum, producing a secretory PLD. Furthermore, we constructed an overexpression system for the secretory enzyme in an active and soluble form using Streptomyces lividans as a host for transformation of the PLD gene. The Stv. cinnamoneum PLD was proven to be useful for the continuous and efficient production of phosphatidylethanolamine (PE) from phosphatidylcholine. Thus, the secretory PLD is a promising catalyst for synthesizing new phospholipids possessing various polar head groups that show versatile physiological functions and may be utilized in food and pharmaceutical industries.     

A kinetic mechanism for the fast movement of Chara myosin

Endoplasmic streaming of characean cells of Nitella or Chara is known to be in the range 30-100 microm/second. The Chara myosin extracted from the cells and fixed onto a glass surface was found to move muscle actin filaments at a velocity of 60 microm/second. This is ten times faster than that of skeletal muscle myosin (myosin II). In this study, the displacement caused by single Chara myosin molecules was measured using optical trapping nanometry. The step size of Chara myosin was approximately 19nm. This step size is longer than that of skeletal muscle myosin but shorter than that of myosin V. The dwell time of the steps was relatively long, and this most likely resulted from two rate-limiting steps, the dissociation of ADP and the binding of ATP. The rate of ADP release from Chara myosin after the completion of the force-generation step was similar to that of myosin V, but was considerably slower than that of skeletal muscle myosin. The 19nm step size and the dwell time obtained could not explain the fast movement. The fast movement could be explained by the load-dependent release of ADP. As the load imposed on the myosin decreased, the rate of ADP release increased. We propose that the interaction of Chara myosin with an actin filament resulted in a negative load being imposed on other myosin molecules interacting with the same actin filament. This resulted in an accelerated release of ADP and the fast sliding movement.     

Bi-directional sex change and gonad structure in the gobiid fish <Emphasis Type="Italic">Trimma yanagitai</Emphasis>

Bi-directional sex change in the deep-water gobiid fish Trimma yanagitai was examined. The gonads of all individuals consisted of ovarian and testicular elements, and an accessory gonadal structure. In no gonads were both testicular and ovarian parts simultaneously active. Bi-directional sex changes occurred during the rearing experiments in aquaria under conditions of which there was co-existence of two males or plural females. The sex of individuals could be determined by their relative body size or social dominance: the largest individuals acting as male and the remainder as female.