Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments

Fossil records indicate that life appeared in marine environments ～3.5 billion years ago (Gyr) and transitioned to terrestrial ecosystems nearly 2.5 Gyr. Sequence analysis suggests that "hydrobacteria" and "terrabacteria" might have diverged as early as 3 Gyr. Bacteria of the genus Azospirillum are associated with roots of terrestrial plants; however, virtually all their close relatives are aquatic. We obtained genome sequences of two Azospirillum species and analyzed their gene origins. While most Azospirillum house-keeping genes have orthologs in its close aquatic relatives, this lineage has obtained nearly half of its genome from terrestrial organisms. The majority of genes encoding functions critical for association with plants are among horizontally transferred genes. Our results show that transition of some aquatic bacteria to terrestrial habitats occurred much later than the suggested initial divergence of hydro- and terrabacterial clades. The birth of the genus Azospirillum approximately coincided with the emergence of vascular plants on land.     

Anionic surfactants in treated sewage and sludges: risk assessment to aquatic and terrestrial environments

Compared to low concentrations of anionic surfactants (AS) in activated sludge process effluents (ASP) (<0.2 mg/L), upflow anaerobic sludge blanket-polishing pond (UASB-PP) effluents were found to contain very high concentrations of AS (>3.5 mg/L). AS (or linear alkylbenzen sulfonate, LAS) removals >99% have been found for ASP while in case of UASB-PP it was found to be < or = 30%. AS concentrations averaged 7347 and 1452 mg/kg dry wt. in wet UASB and dried sludges, respectively. Treated sewage from UASB based sewage treatment plants (STPs) when discharged to aquatic ecosystems are likely to generate substantial risk. Post-treatment using 1-1.6d detention, anaerobic, non-algal polishing ponds was found ineffective. Need of utilizing an aerobic method of post-treatment of UASB effluent in place of an anaerobic one has been emphasized. Natural drying of UASB sludges on sludge drying beds (SDBs) under aerobic conditions results in reduction of adsorbed AS by around 80%. Application of UASB sludges on SDBs was found simple, economical and effective. While disposal of treated UASB effluent may cause risk to aquatic ecosystems, use of dried UASB sludges is not likely to cause risk to terrestrial ecosystems.     

Structural adaptations of the femur and humerus to arboreal and terrestrial environments in three species of macaque

One reason to measure cross-sectional structural properties of primate long bones is to define mechanically relevant complexes of traits that describe the adaptation of bone to different biomechanical environments. This can be effectively accomplished when congeneric species having different postural and locomotor behaviors are compared. This paper compares the cross-sectional geometry of the femur and humerus in three behaviorally different macaque species as a basis for defining such patterns. Cross-sectional moments of inertia in the standard anatomical planes were calculated at five locations along the diaphyses of the femur and humerus in Macaca fascicularis, M. nemestrina, and M. mulatta. The data suggest that the "barrel-shaped" femur is associated with behaviors for which long limbs and small body size are an asset. This may be associated with, but is not restricted to, leaping behaviors. The data also suggest that structural rigidity of the femur and humerus is greater per unit body weight in primates that spend significant amounts of time in terrestrial environments than in those that are more restricted to climbing in arboreal environments.     

Gorilla adaptations to naturalistic environments

In the past few decades there have been increased investigations into the effects of captive environments on behavior. Simultaneously, zoological gardens have undergone a revolution in philosophy and design, resulting in a proliferation of “naturalistic” habitats. Complex environments such as these have been found to affect the behavior of captive animals favorably, including increasing reproductive and rearing success, encouraging the expression of species-typical behavior patterns, and decreasing abnormal behaviors. In June 1988, Zoo Atlanta completed four naturalistic habitats for western lowland gorillas (Gorilla gorilla gorilla). These new habitats afforded a unique opportunity to study the adaptation of lowland gorillas to novel, naturalistic habitats. During the first year of habitation, a total of 451 hours of data were collected on 11 gorillas housed in three harem groups. Focal animal sampling with a behavioral change scoring system was used to obtain information on behavior, substrate, environmental components utilized, and location in sun or shade. Instantaneous scans at 15 minute intervals provided information on location and behavior of all individuals. Adaptation to the environments was assessed by using the indices of: time spent manipulating objects across the course of the study, the percent of the habitats utilized, and the dispersal of individual animals over the habitats. Trends in these behaviors indicated that exploration of the environments significantly decreased, but that this decline in exploration took over six months to occur. Several interpretations of these findings are presented including the unfamiliarity of these naturalistic habitats to these subjects.     

Widespread occurrence of phage-encoded exotoxin genes in terrestrial and aquatic environments in Southern California

Many human diseases are caused by pathogens that produce exotoxins. The genes that encode these exotoxins are frequently encoded by mobile DNA elements such as plasmids or phage. Mobile DNA elements can move exotoxin genes among microbial hosts, converting avirulent bacteria into pathogens. Phage and bacteria from water, soil, and sediment environments represent a potential reservoir of phage- and plasmid-encoded exotoxin genes. The genes encoding exotoxins that are the causes of cholera, diphtheria, enterohemorrhagic diarrhea, and Staphylococcus aureus food poisoning were found in soil, sediment, and water samples by standard PCR assays from locations where the human diseases are uncommon or nonexistent. On average, at least one of the target exotoxin genes was detected in approximately 15% of the more than 300 environmental samples tested. The results of standard PCR assays were confirmed by quantitative PCR (QPCR) and Southern dot blot analyses. Agreement between the results of the standard PCR and QPCR ranged from 63% to 84%; and the agreement between standard PCR and Southern dot blots ranged from 50% to 66%. Both the cholera and shiga exotoxin genes were also found in the free phage DNA fraction. The results indicate that phage-encoded exotoxin genes are widespread and mobile in terrestrial and aquatic environments.     

不同生境下喜旱莲子草营养器官中抗氧化物质含量的比较

以水陆两种生境下生长的喜旱莲子草为实验材料 ,分别测定并比较了根、茎、叶可溶性蛋白及SOD、POD、Vc、GSH及绿原酸和类黄酮等抗氧化物质活性和含量 ,结果表明可溶性蛋白在叶中含量最高 ,并且水生环境中叶的含量高于陆生环境。除Vc外生态环境对各抗氧化物质含量影响具有一致性。水生环境下喜旱莲子草营养器官的抗氧化物质含量高于陆生环境下喜旱莲子草相应营养器官的含量。这是植物体内一种生理生化的生态适应     

Interactions of Vibrio phages and their hosts in aquatic environments

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Excretory nitrogen metabolism in the juvenile axolotl Ambystoma mexicanum: differences in aquatic and terrestrial environments

The fully grown but nonmetamorphosed (juvenile) axolotl Ambystoma mexicanum was ureogenic and primarily ureotelic in water. A complete ornithine-urea cycle (OUC) was present in the liver. Aerial exposure impeded urea (but not ammonia) excretion, leading to a decrease in the percentage of nitrogen excreted as urea in the first 24 h. However, urea and not ammonia accumulated in the muscle, liver, and plasma during aerial exposure. By 48 h, the rate of urea excretion recovered fully, probably due to the greater urea concentration gradient in the kidney. It is generally accepted that an increase in carbamoyl phosphate synthetase activity is especially critical in the developmental transition from ammonotelism to ureotelism in the amphibian. Results from this study indicate that such a transition in A. mexicanum would have occurred before migration to land. Aerial exposure for 72 h exhibited no significant effect on carbamoyl phosphate synthetase-I activity or that of other OUC enzymes (with the exception of ornithine transcarbamoylase) from the liver of the juvenile A. mexicanum. This supports our hypothesis that the capacities of OUC enzymes present in the liver of the aquatic juvenile axolotl were adequate to prepare it for its invasion of the terrestrial environment. The high OUC capacity was further supported by the capability of the juvenile A. mexicanum to survive in 10 mM NH(4)Cl without accumulating amino acids in its body. The majority of the accumulating endogenous and exogenous ammonia was detoxified to urea, which led to a greater than twofold increase in urea levels in the muscle, liver, and plasma and a significant increase in urea excretion by hour 96. Hence, it can be concluded that the juvenile axolotl acquired ureotelism while submerged in water, and its hepatic capacity of urea synthesis was more than adequate to handle the toxicity of endogenous ammonia during migration to land.     

Most probable number quantification of hypophosphite and phosphite oxidizing bacteria in natural aquatic and terrestrial environments

Concentrations of hypophosphite and phosphite oxidizing bacteria were found to be high, relative to bacterial concentrations growing on phosphate, in sediment and soil during winter and summer seasons from 12 common terrestrial and aquatic sites using a most probable number method. The percent of total culturable bacterial concentrations that could use these reduced phosphorus compounds as a sole source of phosphorus were as follows: hypophosphite, 7–100%; phosphite, 10–67%; aminoethylphosphonate, 34–270%. The average MPN/g (±SEM) was as follows: phosphate, 6.19 × 10⁶ (±2.40 × 10⁶); hypophosphite, 2.61 × 10⁶ (±1.35 × 10⁶) phosphite, 1.91 × 10⁶ (±1.02 × 10⁶); aminoethylphosphonate, 3.90 × 10⁶ (± 1.95 × 10⁶). Relatively high concentrations of reduced phosphorus oxidizing bacteria were found in both pristine sites and sites with urban and agricultural disturbance. Concentrations of reduced phosphorus oxidizing bacteria in anoxic sediments and soil were equivalent. Our data indicate that reduced phosphorus oxidizing bacteria are abundant in the environment and provide strong evidence for the importance of bacterial P oxidation in nature.     

Individual adaptations in stochastic environments

Summary Many natural populations undergo radical and unpredictable fluctuations, associated with stochastic environmental conditions. Under such circumstances, fitness of a genotype (or strategy) is defined as the geometric mean of the intergenerational genotypic population growth ratel(t). Unfortunately, this population-level criterion has proved difficult to apply at the level of individual organisms.After developing a formula for the variance ofl as the sum of developmental and environmental variance, we discuss several models of individual adaptations, involving clutch size, progeny size and number, and foraging behaviour under risk of predation, based on the geometric-mean fitness concept. We then show how the method of dynamic programming can be extended to deal with facultative behaviour in stochastic environments. Finally we discuss the concept of an evolutionarily stable strategy in a stochastic environment.Our analysis suggests several novel interpretations of field and laboratory observations. Under the geometric mean criterion behaviour may be determined primarily by the worst likely environment; behaviour may appear suboptimal if observed only under normal or average conditions. For example,except under extreme environmental conditions, avian clutches larger than those that are observed might result in increased fecundity, with little if any cost of reproduction in terms of parental survival; however, in unusually bad years such large clutches might be disastrous, in terms of parental survival. This consideration may help explain some recently reported experimental clutch-size manipulation results. Similarly, our analysis indicates that the known phenomenon of seasonal reduction in seed size may constitute a double bet-hedging strategy, determined by parental mortality risk and future seed survival probability. We also discuss circumstances in which phenotypic polymorphism is an adaptation to environmental uncertainty. Thus almost any individual life history or behavioural adaptation may be affected by environmental stochasticity.     

Risks for overwintering eggs of the dragonfly Sympetrum vicinum in aquatic and terrestrial environments

Hydrobiologia - Risk-spreading behaviour is often exhibited by animals as a response to unpredictably variable environments. Using field and laboratory studies, we tested the hypothesis that...     

Subsidies of long‐chain polyunsaturated fatty acids from aquatic to terrestrial environments via amphibian emergence

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Clonal integration supports the expansion from terrestrial to aquatic environments of the amphibious stoloniferous herb Alternanthera philoxeroides

Effects of clonal integration on land plants have been extensively studied, but little is known about the role in amphibious plants that expand from terrestrial to aquatic conditions. We simulated expansion from terrestrial to aquatic habitats in the amphibious stoloniferous alien invasive alligator weed ( Alternanthera philoxeroides ) by growing basal ramets of clonal fragments in soils connected (allowing integration) or disconnected (preventing integration) to the apical ramets of the same fragments submerged in water to a depth of 0, 5, 10 or 15 cm. Clonal integration significantly increased growth and clonal reproduction of the apical ramets, but decreased both of these characteristics in basal ramets. Consequently, integration did not affect the performance of whole clonal fragments. We propose that alligator weed possesses a double-edged mechanism during population expansion: apical ramets in aquatic habitats can increase growth through connected basal parts in terrestrial habitats; however, once stolon connections with apical ramets are lost by external disturbance, the basal ramets in terrestrial habitats increase stolon and ramet production for rapid spreading. This may contribute greatly to the invasiveness of alligator weed and also make it very adaptable to habitats with heavy disturbance and/or highly heterogeneous resource supply.     

Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments

Background

Adaptation of mammals to terrestrial life was facilitated by the unique vertebrate trait of body hair, which occurs in a range of morphological patterns. Keratin associated proteins (KRTAPs), the major structural hair shaft proteins, are largely responsible for hair variation.

Results

We exhaustively characterized the KRTAP gene family in 22 mammalian genomes, confirming the existence of 30 KRTAP subfamilies evolving at different rates with varying degrees of diversification and homogenization. Within the two major classes of KRTAPs, the high cysteine (HS) subfamily experienced strong concerted evolution, high rates of gene conversion/recombination and high GC content. In contrast, high glycine-tyrosine (HGT) KRTAPs showed evidence of positive selection and low rates of gene conversion/recombination. Species with more hair and of higher complexity tended to have more KRATP genes (gene expansion). The sloth, with long and coarse hair, had the most KRTAP genes (175 with 141 being intact). By contrast, the “hairless” dolphin had 35 KRTAPs and the highest pseudogenization rate (74% relative to the 19% mammalian average). Unique hair-related phenotypes, such as scales (armadillo) and spines (hedgehog), were correlated with changes in KRTAPs. Gene expression variation probably also influences hair diversification patterns, for example human have an identical KRTAP repertoire as apes, but much less hair.

Conclusions

We hypothesize that differences in KRTAP gene repertoire and gene expression, together with distinct rates of gene conversion/recombination, pseudogenization and positive selection, are likely responsible for micro and macro-phenotypic hair diversification among mammals in response to adaptations to ecological pressures.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-779) contains supplementary material, which is available to authorized users.     

The adaptations of fish to extremely alkaline environments

The Lake Magadi Tilapia (MT; Oreochromis alcalicus grahami, the Lahontan cutthroat trout (LCT; Oncorhynchus clarki henshawi) and the tarek (Ct; Chalcalburnus tarichi) have evolved unique strategies that allow them to overcome problems associated with ammonia excretion (J_Amm) and acid-base regulation in their alkaline environments. In Lake Magadi, Kenya (pH 10), the MT circumvents problems associated with J_Amm by excreting virtually all (>90%) of its waste-nitrogen as urea. Base excretion appears to be facilitated by modified seawater-type gill chloride cells, through apical Cl⁻/HCO₃⁻ exchangers and an outwardly directed OH⁻/HCO₃⁻/CO₃⁼ excretion system. The LCT avoids potentially toxic increases in internal ammonia by permanently lowering ammonia production rates following transfer into alkaline (pH 9.4) Pyramid Lake, Nevada, from its juvenile freshwater (pH 8.4) environment. Greater apical exposure of LCT gill chloride cells, presumably the freshwater variety, probably facilitates base excretion by elevating Cl⁻/HCO₃⁻ exchange capacity. In Lake Van, Turkey (pH 9.8) high ammonia tolerance enables C. tarichi to withstand the high internal ammonia concentrations that it apparently requires for the facilitation of J_Amm. It also excretes unusually high amounts of urea. We conclude that adjustments to nitrogenous waste metabolism and excretion patterns, as well as modifications to gill functional morphology, are necessary adaptations that permit these animals to thrive in environments considered unsuitable for most fishes.     

Hydrogenosomes: eukaryotic adaptations to anaerobic environments.

Like mitochondria, hydrogenosomes compartmentalize crucial steps of eukaryotic energy metabolism; however, this compartmentalization differs substantially between mitochondriate aerobes and hydrogenosome-containing anaerobes. Because hydrogenosomes have arisen independently in different lineages of eukaryotic microorganisms, comparative analysis of the various types of hydrogenosomes can provide insights into the functional and evolutionary aspects of compartmentalized energy metabolism in unicellular eukaryotes.     

Olfactory receptors in aquatic and terrestrial vertebrates

In species representing different levels of vertebrate evolution, olfactory receptor genes have been identified by molecular cloning techniques. Comparing the deduced amino-acid sequences revealed that the olfactory receptor gene family of Rana esculenta resembles that of Xenopus laevis, indicating that amphibians in general may comprise two classes of olfactory receptors. Whereas teleost fish, including the goldfish Carassius auratus, possess only class I receptors, the `living fossil' Latimeria chalumnae is endowed with both receptor classes; interestingly, most of the class II genes turned out to be pseudogenes. Exploring receptor genes in aquatic mammals led to the discovery of a large array of only class II receptor genes in the dolphin Stenella Coeruleoalba; however, all of these genes were found to be non-functional pseudogenes. These results support the notion that class I receptors may be specialized for detecting water-soluble odorants and class II receptors for recognizing volatile odorants. Comparing the structural features of both receptor classes from various species revealed that they differ mainly in their extracellular loop 3, which may contribute to ligand specificity. Comparing the number and diversity of olfactory receptor genes in different species provides insight into the origin and the evolution of this unique gene family. Accepted: 29 July 1998     

Growth rates and morphological adaptations of aquatic and terrestrial forms of amphibious Littorella uniflora (L.) Aschers.

Morphological – anatomical features of the terrestrial and the aquatic life form of the rosette species Littorella uniflora, inhabiting nutrient poor soils of oligotrophic lakes, were investigated together with growth rates of both life forms and of transplants. Growth rates were the same for the two life forms. However, growth of transplanted plants was somewhat reduced by transition from one environment to another. This was especially true for aquatic plants, which may be stressed by desiccation when moved to the terrestrial environment. The morphological – anatomical differences between the life forms were small compared with many other amphibious species which produce highly specialized leaves and life forms in air and under water. It is suggested that the conservative leaf morphology of Littorella is a consequence of the high dependence on rhizospheric CO₂ of both the aquatic and the terrestrial form of Littorella, making production of leaves specialized for carbon uptake in one specific environment unnecessary.