Wide geographic distribution of bacteriophages that lyse the same indigenous freshwater isolate (Sphingomonas sp. strain B18)

An indigenous freshwater bacterium (Sphingomonas sp. strain B18) from Lake Plubetasee (Schleswig-Holstein, Germany) was used to isolate 44 phages from 13 very different freshwater and brackish habitats in distant geographic areas. This bacterial strain was very sensitive to a broad spectrum of phages from different aquatic environments. Phages isolated from geographically distant aquatic habitats, but also those from the same sample, were diverse with respect to morphology and restriction pattern. Some phages were widely distributed, while different types coexisted in the same sample. It was concluded that phages could be a major factor in shaping the structure of bacterial communities and maintaining a high bacterial diversity.     

Wide Geographic Distribution of Bacteriophages That Lyse the Same Indigenous Freshwater Isolate (Sphingomonas sp. Strain B18)

An indigenous freshwater bacterium (Sphingomonas sp. strain B18) from Lake Pluβsee (Schleswig-Holstein, Germany) was used to isolate 44 phages from 13 very different freshwater and brackish habitats in distant geographic areas. This bacterial strain was very sensitive to a broad spectrum of phages from different aquatic environments. Phages isolated from geographically distant aquatic habitats, but also those from the same sample, were diverse with respect to morphology and restriction pattern. Some phages were widely distributed, while different types coexisted in the same sample. It was concluded that phages could be a major factor in shaping the structure of bacterial communities and maintaining a high bacterial diversity.     

Diversity and vertical distribution of magnetotactic bacteria along chemical gradients in freshwater microcosms

The vertical distribution of magnetotactic bacteria along various physico-chemical gradients in freshwater microcosms was analyzed by a combined approach of viable cell counts, 16S rRNA gene analysis, microsensor profiling and biogeochemical methods. The occurrence of magnetotactic bacteria was restricted to a narrow sediment layer overlapping or closely below the maximum oxygen and nitrate penetration depth. Different species showed different preferences within vertical gradients, but the largest proportion (63-98%) of magnetotactic bacteria was detected within the suboxic zone. In one microcosm the community of magnetotactic bacteria was dominated by one species of a coccoid "Alphaproteobacterium", as detected by denaturing gradient gel electrophoresis in sediment horizons from 1 to 10 mm depth. Maximum numbers of magnetotactic bacteria were up to 1.5 x 10(7) cells/cm3, which corresponded to 1% of the total cell number in the upper sediment layer. The occurrence of magnetotactic bacteria coincided with the availability of significant amounts (6-60 microM) of soluble Fe(II), and in one sample with hydrogen sulfide (up to 40 microM). Although various trends were clearly observed, a strict correlation between the distribution of magnetotactic bacteria and individual geochemical parameters was absent. This is discussed in terms of metabolic adaptation of various strains of magnetotactic bacteria to stratified sediments and diversity of the magnetotactic bacterial communities.     

Anaerobic methanotrophy is stimulated by graphene oxide in a brackish urban canal sediment

Anthropogenic activities are influencing aquatic environments through increased chemical pollution and thus are greatly affecting the biogeochemical cycling of elements. This has increased greenhouse gas emissions, particularly methane, from lakes, wetlands, and canals. Most of the methane produced in anoxic sediments is converted into carbon dioxide by methanotrophs before it reaches the atmosphere. Anaerobic oxidation of methane requires an electron acceptor such as sulphate, nitrate, or metal oxides. Here, we explore the anaerobic methanotrophy in sediments of three urban canals in Amsterdam, covering a gradient from freshwater to brackish conditions. Biogeochemical analysis showed the presence of a shallow sulphate–methane transition zone in sediments of the most brackish canal, suggesting that sulphate could be a relevant electron acceptor for anaerobic methanotrophy in this setting. However, sediment incubations amended with sulphate or iron oxides (ferrihydrite) did not lead to detectable rates of methanotrophy. Despite the presence of known nitrate-dependent anaerobic methanotrophs (Methanoperedenaceae), no nitrate-driven methanotrophy was observed in any of the investigated sediments either. Interestingly, graphene oxide stimulated anaerobic methanotrophy in incubations of brackish canal sediment, possibly catalysed by anaerobic methanotrophs of the ANME-2a/b clade. We propose that natural organic matter serving as electron acceptor drives anaerobic methanotrophy in brackish sediments.     

Identification and characterization of magnetotactic Gammaproteobacteria from a salt evaporation pool,Bohai Bay,China

Magnetotactic bacteria (MTB) are phylogenetically diverse prokaryotes that can produce intracellular chain-assembled nanocrystals of magnetite (Fe₃O₄) or greigite (Fe₃S₄). Compared with their wide distribution in the Alpha-, Eta- and Delta-proteobacteria classes, few MTB strains have been identified in the Gammaproteobacteria class, resulting in limited knowledge of bacterial diversity and magnetosome biomineralization within this phylogenetic branch. Here, we identify two magnetotactic Gammaproteobacteria strains (tentatively named FZSR-1 and FZSR-2 respectively) from a salt evaporation pool in Bohai Bay, at the Fuzhou saltern, Dalian City, eastern China. Phylogenetic analysis indicates that strain FZSR-2 is the same species as strains SHHR-1 and SS-5, which were discovered previously from brackish and hypersaline environments respectively. Strain FZSR-1 represents a novel species. Compared with strains FZSR-2, SHHR-1 and SS-5 in which magnetite particles are assembled into a single chain, FZSR-1 cells form relatively narrower magnetite nanoparticles that are often organized into double chains. We find a good relationship between magnetite morphology within strains FZSR-2, SHHR-1 and SS-5 and the salinity of the environment in which they live. This study expands the bacterial diversity of magnetotactic Gammaproteobacteria and provides new insights into magnetosome biomineralization within magnetotactic Gammaproteobacteria.     

Single-step transfer of biosynthetic operons endows a non-magnetotactic Magnetospirillum strain from wetland with magnetosome biosynthesis

The magnetotactic lifestyle represents one of the most complex traits found in many bacteria from aquatic environments and depends on magnetic organelles, the magnetosomes. Genetic transfer of magnetosome biosynthesis operons to a non-magnetotactic bacterium has only been reported once so far, but it is unclear whether this may also occur in other recipients. Besides magnetotactic species from freshwater, the genus Magnetospirillum of the Alphaproteobacteria also comprises a number of strains lacking magnetosomes, which are abundant in diverse microbial communities. Their close phylogenetic interrelationships raise the question whether the non-magnetotactic magnetospirilla may have the potential to (re)gain a magnetotactic lifestyle upon acquisition of magnetosome gene clusters. Here, we studied the transfer of magnetosome gene operons into several non-magnetotactic environmental magnetospirilla. Single-step transfer of a compact vector harbouring >30 major magnetosome genes from M. gryphiswaldense induced magnetosome biosynthesis in a Magnetospirillum strain from a constructed wetland. However, the resulting magnetic cellular alignment was insufficient for efficient magnetotaxis under conditions mimicking the weak geomagnetic field. Our work provides insights into possible evolutionary scenarios and potential limitations for the dissemination of magnetotaxis by horizontal gene transfer and expands the range of foreign recipients that can be genetically magnetized.     

Marine invasions by non-sea snakes, with thoughts on terrestrial-aquatic-marine transitions

Few species of snakes show extensive adaptations to aquatic environments and even fewer exploit the oceans. A survey of morphology, lifestyles, and habitats of 2552 alethenophidian snakes revealed 362 (14%) that use aquatic environments, are semi-aquatic, or aquatic; about 70 (2.7%) of these are sea snakes (Hydrophiinae and Laticaudinae). The ancient and aquatic family Acrochordidae contains three extant species, all of which have populations inhabiting brackish or marine environments, as well as freshwater. The Homalopsidae have the most ecologically diverse representatives in coastal habitats. Other families containing species exploiting saline waters with populations in freshwater environments include: the Dipsadidae of the western hemisphere, the cosmopolitan Natricidae, the African Grayinae, and probably a few Colubridae. Species with aquatic and semi-aquatic lifestyles are compared with more terrestrial (fossorial, cryptozoic, and arboreal) species for morphological traits and life histories that are convergent with those found in sea snakes; this may provide clues to the evolution of marine snakes and increase our understanding of snake diversity.     

Ultrastructure of a magnetotactic spirillum.

The ultrastructure of a magnetotactic bacterium (strain MS-1) was examined by transmission, scanning, and scanning-transmission electron microscopy. The organism resembled other spirilla in general cell morphology, although some differences were detected at the ultrastructural level. Electron-dense particles within magnetotactic cells were shown by energy-dispersive X-ray analysis to be localizations containing iron. A non-magnetotactic variant of strain MS-1 lacked these novel bacterial inclusion bodies. A chain of these particles traversed each magnetotactic cell in a specific arrangement that was consistent from cell to cell, seemingly associated with the inner surface of the cytoplasmic membrane. Each particle was surrounded by an electron-dense layer separated from the particle surface by an electron-transparent region. The term "magnetosome" is proposed for the electron-dense particles with their enveloping layer(s) as found in this and other magnetotactic bacteria.     

Combined approach for characterization of uncultivated magnetotactic bacteria from various aquatic environments

Both magnetic collection and "race track" purification techniques were highly effective for selective enrichment of magnetotactic bacteria (MTB) from complex communities, as suggested by amplified ribosomal DNA restriction analysis and denaturing gradient gel electrophoresis combined with sequence analysis of 16S rRNA genes. Using these purification methods, the occurrence and diversity of MTB in microcosms from various marine and freshwater environments were assayed by using a combined microscopic, molecular, and cultivation approach. Most microcosms were dominated by magnetotactic cocci. Consistently, the majority of retrieved 16S RNA sequences were affiliated with a distinct cluster in the Alphaproteobacteria. Within this lineage the levels of sequence divergence were <1 to 11%, indicating genus-level diversity between magnetotactic cocci from various microcosms, as well as between MTB from different stages of succession of the same microcosms. The community composition in microscosms underwent drastic succession during incubation, and significant heterogeneities were observed between microcosms from the same environmental sources. A novel magnetotactic rod (MHB-1) was detected in a sediment sample from a lake in northern Germany by fluorescence in situ hybridization. MHB-1 falls into the Nitrospira phylum, displaying 91% 16S rRNA sequence similarity to "Magnetobacterium bavaricum." In extensive cultivation attempts, we failed to isolate MHB-1, as well as most other MTB present in our samples. However, although magnetotactic spirilla were not frequently observed in the enrichments, 10 novel isolates of the genus Magnetospirillum which had not routinely been isolated in pure culture before were obtained.     

Isolation and characterization of <Emphasis Type="Italic">Magnetospirillum</Emphasis> from saline lagoon

Magnetotactic bacteria (MTB) are aquatic prokaryotes that orient themselves to earth’s magnetic field with the help of intracellular organelle magnetosomes. Although many species of MTB have been identified, the isolation of MTB is a challenging task due to the lack of systematic isolation procedure and/or commercial media. In this study, we are reporting the isolation of magnetotactic spirillum from the Pulicat lagoon, India using a systematic and selective procedure. Sampling site was chosen on the basis of physicochemical properties of the ecosystem and the catalysed reporter deposition fluorescence in situ hybridization (CARD–FISH) analysis of sediment samples. In the current study, a combination of techniques including ‘capillary racetrack’ Purification and gradient cultivation resulted in the isolation of magnetotactic spirilla from aquatic sediments. Based on the 16S rRNA gene sequence analysis, the strain was identified as Magnetospirillum and was designated as Magnetospirillum sp. VITRJS1. The genes responsible for magnetosome formation (mamA, B, E, F, K, M, O, P, Q, T) were successfully detected using PCR amplification. The presence of cbbM gene confirmed that the isolate is chemolithoautotroph and utilises reduced sulphur as an electron source. Furthermore, magnetosomes extracted from VITRJS1 found to be cubo-octahedral in shape and 45 nm in size. Our results indicate that the systematic procedure using sediment analysis, CARD–FISH, and a combination of isolation methods enables the selective and rapid isolation of MTB from aquatic sediment sample.     

Effects of salinity on the life history and fitness of Daphnia magna: variability within and between populations

The life history traits of Daphnia magna were studied in laboratory experiments under freshwater and brackish (5 salinity) conditions. The variability of responses within and between populations was examined by comparing 11 clones from a brackish lake and 10 clones from a freshwater pond. Experimental clones were hatched from ephippia collected from the sediment and thus represent random samples of the clone banks of each population.Most clones with a high salinity tolerance were from the population of the brackish habitat, but some were also found in the freshwater population. Thus, freshwater populations appear to have the potential to invade brackish habitats. A proportion of clones from the brackish population had very low fitness (measured as e^r) under freshwater conditions. This unexpected result means that freshwater adaptation can be lost by the freshwater cladoceran Daphnia magna. The effects of unfavourable conditions on growth and reproduction varied among clones and were not correlated. This clonal variation in growth and reproduction indicates that the environmental sensitivities of these traits are independent. The pattern of fitness reaction norms showed no trade-off between fitness under brackish and under freshwater conditions for either population. Thus, euryhaline generalists should be favoured in habitats with salinity fluctuations between freshwater and brackish conditions.     

Species diversity of magnetotactic bacteria from the Ol’khovka River, Russia

A fraction of magnetotactic bacteria was isolated by magnetic separation from the water and silt samples collected from the Ol’khovka River (Kislovodsk, Russia). A 16S rRNA clone library was obtained from the total DNA of the fraction by PCR amplification and molecular cloning. Phylogenetic analysis of 67 16S rRNA gene sequences of randomly selected clones demonstrated that two phylotypes of magnetotactic bacteria were present in the library: the first phylotype consisted of 42 sequences and the second one included only one sequence. The remaining 24 sequences belonged to non-magnetotactic bacteria. According to the results of phylogenetic analysis, both phylotypes were magnetotactic cocci; the predominant sequences were almost identical to the 16S rRNA sequence of the freshwater coccus TB24 (X81185.1) identified earlier among the magnetotactic bacteria isolated from Lake Chiemsee (Bavaria). The phylotype represented by a single sequence formed a separate branch in the dendrogram, with 97% similarity between its sequence and that of TB24. The discovered phylotypes formed with the sequences of uncultured freshwater magnetotactic cocci a separate branch within the class Alphaproteobacteria and presumably belonged to a separate family within the recently described order Magnetococcales. Despite the fact that phylogenetic analysis of the 16S rRNA clone library did not reveal any phylotypes of magnetotactic spirilla, after the secondary enrichment of the fraction of magnetotactic bacteria using the “race track” technique, a new strain of magnetotactic spirilla, Magnetospirillum SO-1, was isolated. The closest relative of strain SO-1 was the previously described magnetotactic spirillum Magnetospirillum magneticum AMB-1.     

A biogeographic distribution of magnetotactic bacteria influenced by salinity

Magnetotactic bacteria (MTB), which synthesize intracellular ferromagnetic magnetite and/or greigite magnetosomes, have significant roles in global iron cycling in aquatic systems, as well as sedimentary magnetism. The occurrence of MTB has been reported in aquatic environments from freshwater to marine ecosystems; however, the distribution of MTB across heterogeneous habitats remains unclear. Here we examined the MTB communities from diverse habitats across northern and southern China, using comprehensive transmission electron microscopy and comparison of 16S rRNA gene analyses. A total of 334 16S rRNA gene sequences were analyzed, representing the most comprehensive analysis on the diversity and distribution of MTB to date. The majority (95%) of sequences belong to the Alphaproteobacteria, whereas a population of giant magnetotactic rod is affiliated with the Nitrospirae phylum. By a statistical comparison of these sequence data and publicly available MTB sequences, we infer for the first time that the composition of MTB communities represents a biogeographic distribution across globally heterogeneous environments, which is influenced by salinity.     

Combined Approach for Characterization of Uncultivated Magnetotactic Bacteria from Various Aquatic Environments

Both magnetic collection and “race track” purification techniques were highly effective for selective enrichment of magnetotactic bacteria (MTB) from complex communities, as suggested by amplified ribosomal DNA restriction analysis and denaturing gradient gel electrophoresis combined with sequence analysis of 16S rRNA genes. Using these purification methods, the occurrence and diversity of MTB in microcosms from various marine and freshwater environments were assayed by using a combined microscopic, molecular, and cultivation approach. Most microcosms were dominated by magnetotactic cocci. Consistently, the majority of retrieved 16S RNA sequences were affiliated with a distinct cluster in the Alphaproteobacteria. Within this lineage the levels of sequence divergence were <1 to 11%, indicating genus-level diversity between magnetotactic cocci from various microcosms, as well as between MTB from different stages of succession of the same microcosms. The community composition in microscosms underwent drastic succession during incubation, and significant heterogeneities were observed between microcosms from the same environmental sources. A novel magnetotactic rod (MHB-1) was detected in a sediment sample from a lake in northern Germany by fluorescence in situ hybridization. MHB-1 falls into the Nitrospira phylum, displaying 91% 16S rRNA sequence similarity to “Magnetobacterium bavaricum.” In extensive cultivation attempts, we failed to isolate MHB-1, as well as most other MTB present in our samples. However, although magnetotactic spirilla were not frequently observed in the enrichments, 10 novel isolates of the genus Magnetospirillum which had not routinely been isolated in pure culture before were obtained.     

Historical changes in the aquatic environment and input of polycyclic aromatic hydrocarbons over 1000 years in Lake Kitaura,Japan

We examined the vertical distributions of total organic carbon (TOC), total nitrogen (TN), total sulfur (TS), and 21 polycyclic aromatic hydrocarbons (PAHs) in a 100-cm-long sediment core collected from Lake Kitaura, a small and shallow eutrophic freshwater lake in central Japan, to elucidate changes in its aquatic environment and the input of PAHs with respect to human activity over the last 1000 years. Using a cross-plot of TOC and TS, the aquatic environment of this lake was well classified into four stages: a marine–brackish water period (≤1321 AD), a brackish–freshwater period (1394–1646 AD), a freshwater period (1726–1958 AD), and a eutrophication period (≥1971 AD). During the current eutrophication period, both TOC and TN have increased dramatically and TOC/TN (which is a useful indicator for distinguishing between aquatic and terrestrial plant sources) has decreased because algal production has markedly increased recently due to eutrophication. The vertical distributions of PAHs (which have derived primarily from combustion over the last 1000 years) showed increases in layers corresponding to periods of volcanic activity in the 18th century, as well as dramatic increases from 1971 to the present. Thus, both the aquatic environment and the input of PAHs in Lake Kitaura have been strongly affected by recent human activity. On the other hand, among all of the PAHs, only perylene—which is known to be of biological origin—was consistently formed via first-order kinetics over the period covered by the core. Its formation was barely influenced by fluctuations in the input of the precursor of perylene or how reductive the environment in the bottom water was.     

Isolation of obligately alkaliphilic magnetotactic bacteria from extremely alkaline environments

Large numbers of magnetotactic bacteria were discovered in mud and water samples collected from a number of highly alkaline aquatic environments with pH values of ≈ 9.5. These bacteria were helical in morphology and biomineralized chains of bullet-shaped crystals of magnetite and were present in all the highly alkaline sites sampled. Three strains from different sites were isolated and cultured and grew optimally at pH 9.0-9.5 but not at 8.0 and below, demonstrating that these organisms truly require highly alkaline conditions and are not simply surviving/growing in neutral pH micro-niches in their natural habitats. All strains grew anaerobically through the reduction of sulfate as a terminal electron acceptor and phylogenetic analysis, based on 16S rRNA gene sequences, as well as some physiological features, showed that they could represent strains of Desulfonatronum thiodismutans, a known alkaliphilic bacterium that does not biomineralize magnetosomes. Our results show that some magnetotactic bacteria can be considered extremophilic and greatly extend the known ecology of magnetotactic bacteria and the conditions under which they can biomineralize magnetite. Moreover, our results show that this type of magnetotactic bacterium is common in highly alkaline environments. Our findings also greatly influence the interpretation of the presence of nanometer-sized magnetite crystals, so-called magnetofossils, in highly alkaline environments.     

Genetic and morphometric divergence in threespine stickleback in the Chignik catchment,Alaska

Divergent selection pressures induced by different environmental conditions typically lead to variation in life history, behavior, and morphology. When populations are locally adapted to their current environment, selection may limit movement into novel sites, leading to neutral and adaptive genetic divergence in allopatric populations. Subsequently, divergence can be reinforced by development of pre‐ or postzygotic barriers to gene flow. The threespine stickleback, Gasterosteus aculeatus, is a primarily marine fish that has invaded freshwater repeatedly in postglacial times. After invasion, the established freshwater populations typically show rapid diversification of several traits as they become reproductively isolated from their ancestral marine population. In this study, we examine the genetic and morphometric differentiation between sticklebacks living in an open system comprising a brackish water lagoon, two freshwater lakes, and connecting rivers. By applying a set of microsatellite markers, we disentangled the genetic relationship of the individuals across the diverse environments and identified two genetic populations: one associated with brackish and the other with the freshwater environments. The “brackish” sticklebacks were larger and had a different body shape than those in freshwater. However, we found evidence for upstream migration from the brackish lagoon into the freshwater environments, as fish that were genetically and morphometrically similar to the lagoon fish were found in all freshwater sampling sites. Regardless, few F1‐hybrids were identified, and it therefore appears that some pre‐ and/or postzygotic barriers to gene flow rather than geographic distance are causing the divergence in this system.     

The effects of environmental salinity on trunk kidney proteome of juvenile ayu (Plecoglossus altivelis)

As the life cycle of ayu spans river, brackish and seawater environments, it would be a suitable fish model for studying the responses to salinity changes in aquatic animals. We investigated the effect of salinity on trunk kidney proteome in ayu (Plecoglossus altivelis) using two-dimensional gel electrophoresis and mass spectrometry. The proteins involved in the process of energy metabolism, biosynthesis, DNA methylation and cell differentiation were mainly affected, and 10 significantly changed proteins were identified. Our result showed that isocitrate dehydrogenase (ICD), pyruvate dehydrogenase (E1), O-glycosyl hydrolase, mitochondrial precursor of ATP synthase subunit beta, mitochondrial ferrtin (MtF), retinol binding protein (RBP) were down-regulated, whereas aldehyde dehydrogenase, cytokeratin 1, S-adenosylhomocysteine hydrolase, Cys-Met metabolism PLP-dependent enzyme were up-regulated when ayu transferred from freshwater to brackish water. Partial coding sequences of E1, ICD, MtF and RBP genes were determined, and the effects of salinity on their mRNA expression in ayu trunk kidney were tested by real-time PCR subsequently. Their possible direct or indirect roles in the adaptation of ayu to salinity are discussed.     

Bryozoans are returning home: recolonization of freshwater ecosystems inferred from phylogenetic relationships

Bryozoans are aquatic invertebrates that inhabit all types of aquatic ecosystems. They are small animals that form large colonies by asexual budding. Colonies can reach the size of several tens of centimeters, while individual units within a colony are the size of a few millimeters. Each individual within a colony works as a separate zooid and is genetically identical to each other individual within the same colony. Most freshwater species of bryozoans belong to the Phylactolaemata class, while several species that tolerate brackish water belong to the Gymnolaemata class. Tissue samples for this study were collected in the rivers of Adriatic and Danube basin and in the wetland areas in the continental part of Croatia (Europe). Freshwater and brackish taxons of bryozoans were genetically analyzed for the purpose of creating phylogenetic relationships between freshwater and brackish taxons of the Phylactolaemata and Gymnolaemata classes and determining the role of brackish species in colonizing freshwater and marine ecosystems. Phylogenetic relationships inferred on the genes for 18S rRNA, 28S rRNA, COI, and ITS2 region confirmed Phylactolaemata bryozoans as radix bryozoan group. Phylogenetic analysis proved Phylactolaemata bryozoan's close relations with taxons from Phoronida phylum as well as the separation of the Lophopodidae family from other families within the Plumatellida genus. Comparative analysis of existing knowledge about the phylogeny of bryozoans and the expansion of known evolutionary hypotheses is proposed with the model of settlement of marine and freshwater ecosystems by the bryozoans group during their evolutionary past. In this case study, brackish bryozoan taxons represent a link for this ecological phylogenetic hypothesis. Comparison of brackish bryozoan species Lophopus crystallinus and Conopeum seurati confirmed a dual colonization of freshwater ecosystems throughout evolution of this group of animals.