Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11(T))

Chromohalobacter salexigens is one of nine currently known species of the genus Chromohalobacter in the family Halomonadaceae. It is the most halotolerant of the so-called 'moderately halophilic bacteria' currently known and, due to its strong euryhaline phenotype, it is an established model organism for prokaryotic osmoadaptation. C. salexigens strain 1H11(T) and Halomonas elongata are the first and the second members of the family Halomonadaceae with a completely sequenced genome. The 3,696,649 bp long chromosome with a total of 3,319 protein-coding and 93 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2004.     

Complete genome sequence of Hirschia baltica type strain (IFAM 1418(T))

The family Hyphomonadaceae within the Alphaproteobacteria is largely comprised of bacteria isolated from marine environments with striking morphologies and an unusual mode of cell growth. Here, we report the complete genome sequence Hirschia baltica, which is only the second a member of the Hyphomonadaceae with a published genome sequence. H. baltica is of special interest because it has a dimorphic life cycle and is a stalked, budding bacterium. The 3,455,622 bp long chromosome and 84,492 bp plasmid with a total of 3,222 protein-coding and 44 RNA genes were sequenced as part of the DOE Joint Genome Institute Program CSP 2008.     

Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6)

Hydrogenobacter thermophilus Kawasumi et al. 1984 is the type species of the genus Hydrogenobacter. H. thermophilus was the first obligate autotrophic organism reported among aerobic hydrogen-oxidizing bacteria. Strain TK-6(T) is of interest because of the unusually efficient hydrogen-oxidizing ability of this strain, which results in a faster generation time compared to other autotrophs. It is also able to grow anaerobically using nitrate as an electron acceptor when molecular hydrogen is used as the energy source, and able to aerobically fix CO(2)via the reductive tricarboxylic acid cycle. This is the fifth completed genome sequence in the family Aquificaceae, and the second genome sequence determined from a strain derived from the original isolate. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,742,932 bp long genome with its 1,899 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Crop performance, nitrogen and water use in flooded and aerobic rice

Irrigated aerobic rice is a new system being developed for lowland areas with water shortage and for favorable upland areas with access to supplementary irrigation. It entails the cultivation of nutrient-responsive cultivars in nonsaturated soil with sufficient external inputs to reach yields of 70–80% of high-input flooded rice. To obtain insights into crop performance, water use, and N use of aerobic rice, a field experiment was conducted in the dry seasons of 2002 and 2003 in the Philippines. Cultivar Apo was grown under flooded and aerobic conditions at 0 and at 150 kg fertilizer N ha^–1. The aerobic fields were flush irrigated when the soil water potential at 15-cm depth reached –30 kPa. A ¹⁵N isotope study was carried out in microplots within the 150-N plots to determine the fate of applied N. The yield under aerobic conditions with 150 kg N ha^–1 was 6.3 t ha^–1 in 2002 and 4.2 t ha^–1 in 2003, and the irrigation water input was 778 mm in 2002 and 826 mm in 2003. Compared with flooded conditions, the yield was 15 and 39% lower, and the irrigation water use 36 and 41% lower in aerobic plots in 2002 and 2003, respectively. N content at 150 kg N ha^–1 in leaves and total plant was nearly the same for aerobic and flooded conditions, indicating that crop growth under aerobic conditions was limited by water deficit and not by N deficit. Under aerobic conditions, average fertilizer N recovery was 22% in both the main field and the microplot, whereas under flooded conditions, it was 49% in the main field and 36% in the microplot. Under both flooded and aerobic conditions, the fraction of ¹⁵N that was determined in the soil after the growing season was 23%. Since nitrate contents in leachate water were negligible, we hypothesized that the N unaccounted for were gaseous losses. The N unaccounted for was higher under aerobic conditions than under flooded conditions. For aerobic rice, trials are suggested for optimizing dose and timing of N fertilizer. Also further improvements in water regime should be made to reduce crop water stress.     

Aerobic cometabolism of chloroform by butane-grown microorganisms: long-term monitoring of depletion rates and isolation of a high-performing strain

The focus of this microcosm study was to monitor the performances of 17 butane-utilizing microcosms during a long-term (100–250 days) aerobic cometabolic depletion of chloroform (CF). The depletion of the contaminant began after a lag-time variable between 0 and 23 days. All microcosms quickly reached a pseudo steady-state condition, in terms of biomass concentration (with an average of 9.3 × 10⁶ CFU ml^–1), chloroform depletion rate (5 mol l^–1 d^–1) and butane utilization rate (730 mol l^–1 d^–1). After about 100 days of CF depletion, a sudden 5- to 7-fold increase of the chloroform rate was observed in two microcosms, where the highest amount of contaminant had been depleted. In one of these high-performing microcosms, an experiment of chloroform depletion in the absence of butane resulted in the depletion of a surprisingly high amount of contaminant (765 mol_CF kg_{dry soil}^–1 in 2 months) and in a marked selection of a single bacterial strain. Bioaugmentation assays conducted with the biomass selected in this microcosm and with a pure culture of the selected strain immediately resulted in very high chloroform depletion rates. Preliminary results of a study conducted with resting cells of the selected strain indicated that it can degrade chloroform concentrations up to 119 M (14.2 mg l^–1) without any sign of substrate toxicity, and that it is able to transform vinyl chloride and 1,1,2-trichloroethane.     

Selective breeding for high endurance running increases hindlimb symmetry

Comparative studies provide correlational evidence of morphological adaptations for high locomotor performance, such as the classical indicators of cursoriality in mammals, long limbs and high metatarsal/femur ratios. More recently, enlarged femoral condyles have been suggested as an adaptation for high endurance running in the genus Homo. Asymmetry of locomotor appendages should adversely affect locomotor abilities, but this has not been studied in a rigorous evolutionary context. We used experimental evolution to test for morphological adaptations associated with high voluntary wheel running in selectively bred lines of mice. Surprisingly, the classical indicators of cursoriality had not evolved in concert with high activity levels. Instead, high runners had larger femoral condyles and reduced directional asymmetry of hindlimb bones. We hypothesize that greater limb symmetry and larger femoral heads are general adaptations associated with sustained, high-speed locomotion.     

Diving through the thermal window: implications for a warming world

Population decline and a shift in the geographical distribution of some ectothermic animals have been attributed to climatic warming. Here, we show that rises in water temperature of a few degrees, while within the thermal window for locomotor performance, may be detrimental to diving behaviour in air-breathing ectotherms (turtles, crocodilians, marine iguanas, amphibians, snakes and lizards). Submergence times and internal and external body temperature were remotely recorded from freshwater crocodiles (Crocodylus johnstoni) while they free-ranged throughout their natural habitat in summer and winter. During summer, the crocodiles'' mean body temperature was 5.2 ± 0.1°C higher than in winter and the largest proportion of total dive time was composed of dive durations approximately 15 min less than in winter. Diving beyond 40 min during summer required the crocodiles to exponentially increase the time they spent on the surface after the dive, presumably to clear anaerobic debt. The relationship was not as significant in winter, even though a greater proportion of dives were of a longer duration, suggesting that diving lactate threshold (DLT) was reduced in summer compared with winter. Additional evidence for a reduced DLT in summer was derived from the stronger influence body mass exerted upon dive duration, compared to winter. The results demonstrate that the higher summer body temperature increased oxygen demand during the dive, implying that thermal acclimatization of the diving metabolic rate was inadequate. If the study findings are common among air-breathing diving ectotherms, then long-term warming of the aquatic environment may be detrimental to behavioural function and survivorship.     

Involvement of ATP and autoinducer‐2 in aerobic granulation

Aerobic granulation represents an important bacterium‐to‐bacterium self‐immobilization process that has been exploited for the treatment of a wide spectrum of wastewaters, but the mechanism behind still remains unclear in a microbiological sense. This study investigated the possible involvement of ATP and autoinducer‐2 (AI‐2) in aerobic granulation. Results revealed that initiation of microbial aggregation is closely associated with the ATP content of biomass, whereas AI‐2 of biomass would be essential for maturation of aerobic granules. Furthermore, it was found that the AI‐2‐associated coordination of microorganisms in microbial aggregates would be biomass density dependent. This study clearly shows the involvement of ATP and autoinducer‐2 in aerobic granulation, and may be exploited further for enhancement or prevention of microbial aggregation in general, for example, rapid granulation for wastewater treatment or inhibition of biofouling in membrane bioreactor. Biotechnol. Bioeng. 2010;105: 51–58. © 2009 Wiley Periodicals, Inc.