High abundance of planctomycetes in anoxic layers of a Sphagnum peat bog

The depth distribution of planctomycete abundance has been examined in six different sites of the Sphagnum peat bog Bakchar, Tomsk oblast, Russia. In situ hybridization of peat with the fluorescently labeled oligonucleotide probes PLA46 and PLA886, reported to be group-specific for representatives of the phylum Planctomycetes, revealed two distinct population maxima of these bacteria in all of the profiles examined. The first population maximum was detected in the uppermost, oxic layer of the bog profile, while the second maximum was located at a depth of 30 cm below the water table level. The population sizes of planctomycetes in the uppermost layer and at a depth of 30 cm were of the same order of magnitude and comprised 0.5–1.5 × 10⁷ and 0.4?0.7 × 10⁷ cells per g^?1 of wet peat, respectively. Only 25–30% of the total number of planctomycete cells in the anoxic layer could be detected if the probe PLA886, whose target specificity is restricted to taxonomically characterized aerobic planctomycetes of the genera Gemmata, Planctomyces, Pirellula, and Isosphaera, was used alone. Other planctomycete cells in this layer were detected only with the probe PLA46, which possesses a much wider scope. This suggests the affiliation of these organisms with a yet undescribed phylogenetic subgroup within the Planctomycetes.     

High abundance of planctomycetes in anoxic layers of a Sphagnum peat bog

The depth distribution of planctomycete abundance has been examined in six different sites of the Sphagnum peat bog in Bakchar, Tomsk oblast, Russia. In situ hybridization of peat with the fluorescently labeled oligonucleotide probes PLA46 and PLA886, reported to be group-specific for representatives of the phylum Planctomycetes, revealed two distinct population maxima of these bacteria in all of the profiles examined. The first population maximum was detected in the uppermost, oxic layer of the bog profile, while the second maximum was located at a depth of 30 cm below the water table level. The population sizes of planctomycetes in the uppermost layer and at a depth of 30 cm were of the same order of magnitude and comprised 0.5-1.5 x 10(7) and 0.4-0.7 x 10(7) cells per g of wet peat, respectively. Only 25-30% of the total number of planctomycete cells in the anoxic layer could be detected if the probe PLA886, whose target specificity is restricted to taxonomically characterized aerobic planctomycetes of the genera Gemmata, Planctomyces, Pirellula, and Isosphaera, was used alone. Other planctomycete cells in this layer were detected only with the probe PLA46, which possesses a much wider scope. This suggests the affiliation of these organisms with a yet undescribed phylogenetic subgroup within the Planctomycetes.     

Population genetic structure in six sympatric and widespread aquatic plants inhabiting diverse lake environments in China

Many aquatic plant species are distributed over large areas and diverse environments with populations interconnected by abiotic and biotic mediators. Here, we examined differences and similarities in the population genetic structure of six sympatric and widespread aquatic plant species. We sampled the aquatic species from six Chinese lakes found on plateaus, plains, and different river systems and analyzed them using inter‐simple sequence repeat (ISSR) markers. Samples originating from each lake tended to cluster together. Of the six species, only Nymphoides peltata and Myriophyllum spicatum could be divided into plateau and plain groups, once Taihu Lake individuals were excluded. Genetic similarities between populations connected by the Yangtze River were not consistently higher than unconnected populations. Populations from Taihu Lake and/or Weishanhu Lake were distant from other lake populations for all species except Potamogeton lucens. The Taihu and Weishanhu populations clustered for Ceratophyllum demersum and Typha latifolia. Hydrophilous C. demersum had the lowest gene flow (Nm = 0.913), whereas the entomophilous Hydrocharis dubia (Nm = 2.084) and N. peltata (Nm = 2.204) had the highest gene flow. The genetic relationships among distant populations of aquatic plants reflect the comprehensive effects of environmental selection pressure and biotic and abiotic connectivity. Differences in environmental factors between plateau and plain lakes and long distance hydrochory have limited importance on aquatic plant genetic structures. Among multiple evolutionary forces, gene flow mediated by birds may play the most important role in the formation of genetic patterns in the six species examined. For example, the close genetic relationship between Taihu Lake and Weishanhu Lake populations, each in different river systems and with different climates, may be related to the migration routes of birds. Differences in gene flow among the six aquatic plants may be attributable to different bird‐transport and the fruit traits of each species.     

A novel photosynthetic strategy for adaptation to low-iron aquatic environments

Iron (Fe) availability is a major limiting factor for primary production in aquatic environments. Cyanobacteria respond to Fe deficiency by derepressing the isiAB operon, which encodes the antenna protein IsiA and flavodoxin. At nanomolar Fe concentrations, a PSI-IsiA supercomplex forms, comprising a PSI trimer encircled by two complete IsiA rings. This PSI-IsiA supercomplex is the largest photosynthetic membrane protein complex yet isolated. This study presents a detailed characterization of this complex using transmission electron microscopy and ultrafast fluorescence spectroscopy. Excitation trapping and electron transfer are highly efficient, allowing cyanobacteria to avoid oxidative stress. This mechanism may be a major factor used by cyanobacteria to successfully adapt to modern low-Fe environments.     

Phylogeography of Ptychadena mascareniensis suggests transoceanic dispersal in a widespread African-Malagasy frog lineage

Aim The Mascarene ridged frog, Ptychadena mascareniensis, is the only African amphibian species thought to occur on Madagascar and on the Seychelles and also Mascarene islands. We explored its phylogenetic relationships and intraspecific genetic differentiation to contribute to the understanding of transoceanic dispersal in amphibians. Methods Fragments of the mitochondrial 16S rRNA gene were sequenced from specimens collected over most of the distribution area of P. mascareniensis, including populations from Madagascar, Mascarenes and Seychelles. Results We identified five deeply divergent clades having pairwise divergences >5%, which probably all represent cryptic species in a P. mascareniensis complex. One of these seems to be restricted to Madagascar, the Mascarenes and the Seychelles. Sequences obtained from topotypic material (Réunion) were identical to the most widespread haplotype from Madagascar. The single Mauritian/Seychellean haplotype differed by only one mutation from a Malagasy haplotype. Main conclusions It is likely that the Mascarene and Seychellean populations were introduced from Madagascar by humans. In contrast, the absence of the Malagasy haplotypes from Africa and the distinct divergences among Malagasy populations (16 mutations in one divergent hapolotype from northern Madagascar) suggest that Madagascar was populated by Ptychadena before the arrival of humans c. 2000 years ago. Because Madagascar has been separated from Africa since the Jurassic, this colonization must have taken place by overseas rafting, which may be a more widespread dispersal mode in amphibians than commonly thought.     

Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America

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Environmental and genealogical effects on DNA methylation in a widespread apomictic dandelion lineage

DNA methylation in plant genomes occurs in different sequences and genomic contexts that have very different properties. DNA methylation that occurs in CG (mCG) sequence context shows transgenerational stability and high epimutation rate, and can thus provide genealogical information at short time scales. However, due to meta-stability and because mCG variants may arise due to other factors than epimutation, such as environmental stress exposure, it is not clear how well mCG captures genealogical information at micro-evolutionary time scales. Here, we analysed DNA methylation variation between accessions from a geographically widespread, apomictic common dandelion (Taraxacum officinale) lineage when grown experimentally under different light conditions. Using a reduced-representation bisulphite sequencing approach, we show that the light treatment induced differentially methylated cytosines (DMCs) in all sequence contexts, with a bias towards transposable elements. Accession differences were associated mainly with DMCs in CG context. Hierarchical clustering of samples based on total mCG profiles revealed a perfect clustering of samples by accession identity, irrespective of light conditions. Using microsatellite information as a benchmark of genetic divergence within the clonal lineage, we show that genetic divergence between accessions correlates strongly with overall mCG profiles. However, our results suggest that environmental effects that do occur in CG context may produce a heritable signal that partly dilutes the genealogical signal. Our study shows that methylation information in plants can be used to reconstruct micro-evolutionary genealogy, providing a useful tool in systems that lack genetic variation such as clonal and vegetatively propagated plants.     

No population genetic structure in a widespread aquatic songbird from the Neotropics

Neotropical lowland organisms often show marked population genetic structure, suggesting restricted migration among populations. However, most phylogeographic studies have focused on species inhabiting humid forest interior. Little attention has been devoted to the study of species with ecologies conducive to dispersal, such as those of more open and variable environments associated with watercourses. Using mtDNA sequences, we examined patterns of genetic variation in a widely distributed Neotropical songbird of aquatic environments, the Yellow-hooded Blackbird (Icteridae, Chrysomus icterocephalus). In contrast to many forest species, Yellow-hooded Blackbirds showed no detectable genetic structure across their range, which includes lowland populations on both sides of the Andes, much of northeastern South America, Amazonia, as well as a phenotypically distinct highland population in Colombia. A coalescent-based analysis of the species indicated that its effective population size has increased considerably, suggesting a range expansion. Our results support the hypothesis that species occurring in open habitats and tracking temporally dynamic environments should show increased dispersal propensities (hence gene flow) relative to species from closed and more stable environments. The phenotypic and behavioral variation among populations of our study species appears to have arisen recently and perhaps in the face of gene flow.     

Syntrophic growth on formate: a new microbial niche in anoxic environments

Anaerobic syntrophic associations of fermentative bacteria and methanogenic archaea operate at the thermodynamic limits of life. The interspecies transfer of electrons from formate or hydrogen as a substrate for the methanogens is key. Contrary requirements of syntrophs and methanogens for growth-sustaining product and substrate concentrations keep the formate and hydrogen concentrations low and within a narrow range. Since formate is a direct substrate for methanogens, a niche for microorganisms that grow by the conversion of formate to hydrogen plus bicarbonate--or vice versa--may seem unlikely. Here we report experimental evidence for growth on formate by syntrophic communities of (i) Moorella sp. strain AMP in coculture with a thermophilic hydrogen-consuming Methanothermobacter species and of (ii) Desulfovibrio sp. strain G11 in coculture with a mesophilic hydrogen consumer, Methanobrevibacter arboriphilus AZ. In pure culture, neither Moorella sp. strain AMP, nor Desulfovibrio sp. strain G11, nor the methanogens grow on formate alone. These results imply the existence of a previously unrecognized microbial niche in anoxic environments.     

Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages

Cyanobacteria are often the dominant phototrophs in polar freshwater communities; yet, the phages that infect them remain unknown. Here, we present a genomic and morphological characterization of cyanophage S-EIV1 that was isolated from freshwaters on Ellesmere Island (Nunavut, High Arctic Canada), and which infects the polar Synechococcus sp., strain PCCC-A2c. S-EIV1 represents a newly discovered evolutionary lineage of bacteriophages whose representatives are widespread in aquatic systems. Among the 130 predicted open reading frames (ORFs) there is no recognizable similarity to genes that encode structural proteins other than the large terminase subunit and a distant viral morphogenesis protein, indicating that the genes encoding the structural proteins of S-EIV1 are distinct from other viruses. As well, only 19 predicted coding sequences on the 79 178 bp circularly permuted genome have homology with genes encoding proteins of known function. Although S-EIV1 is divergent from other sequenced phage isolates, it shares synteny with phage genes captured on a fosmid from the deep-chlorophyll maximum in the Mediterranean Sea, as well as with an incision element in the genome of Anabaena variabilis (ATCC 29413). Sequence recruitment of metagenomic data indicates that S-EIV1-like viruses are cosmopolitan and abundant in a wide range of aquatic systems, suggesting they have an important ecological role.     

Experimental biology of ammonia-rich environments. Germination of allium seed, a novel capability among angiosperms

Seed populations from a majority of species and cultivars of Allium yield up to 15% germination under atmospheres containing NH₃ together with equal volumes of N₂ or air. Selected onion and leek cultivars tested in a range of NH₃ or O₂ compositions show little or no dependency upon quantitative variations in these gases.     

Intraguild predation: a widespread interaction related to species biology

Intraguild predation (IGP), defined as killing and eating among potential competitors, seems to be a ubiquitous interaction, differing from competition or predation. In the present study we assess the frequency of IGP among 763 potential intraguild prey and 599 potential intraguild predators. Our results indicate that IGP is common in nature, reaching frequencies between 58.4 and 86.7%. A null model suggests that IGP in different groups of predators and prey (i.e. carnivores, omnivores, herbivores, detritivores, or top and intermediate species) have different deviations from a chance expectation, indicating these attributes of species biology as main determinants of IGP persistence. We suggest that IGP satisfies two basic requirements to be considered as important to the trophic structuring of communities. First, its occurrence is not random, rather it is associated with well‐defined attributes of species biology, and secondly, it is a widespread interaction.     

Biogeochemistry and microbial ecology of methane oxidation in anoxic environments: a review

Evidence supporting a key role for anaerobic methane oxidation in the global methane cycle is reviewed. Emphasis is on recent microbiological advances. The driving force for research on this process continues to be the fact that microbial communities intercept and consume methane from anoxic environments, methane that would otherwise enter the atmosphere. Anaerobic methane oxidation is biogeochemically important because methane is a potent greenhouse gas in the atmosphere and is abundant in anoxic environments. Geochemical evidence for this process has been observed in numerous marine sediments along the continental margins, in methane seeps and vents, around methane hydrate deposits, and in anoxic waters. The anaerobic oxidation of methane is performed by at least two phylogenetically distinct groups of archaea, the ANME-1 and ANME-2. These archaea are frequently observed as consortia with sulfate-reducing bacteria, and the metabolism of these consortia presumably involves a syntrophic association based on interspecies electron transfer. The archaeal member of a consortium apparently oxidizes methane and shuttles reduced compounds to the sulfate-reducing bacteria. Despite recent advances in understanding anaerobic methane oxidation, uncertainties still remain regarding the nature and necessity of the syntrophic association, the biochemical pathway of methane oxidation, and the interaction of the process with the local chemical and physical environment. This review will consider the microbial ecology and biogeochemistry of anaerobic methane oxidation with a special emphasis on the interactions between the responsible organisms and their environment. This revised version was published online in August 2006 with corrections to the Cover Date.     

Ecology of Vibrio mimicus in aquatic environments

An environmental study was done to examine the prevalence of Vibrio mimicus in some aquatic environments of Dhaka, Bangladesh, and of Okayama, Japan. Water samples from Dhaka environments and water and plankton samples from Okayama environments were quantitatively as well as qualitatively analyzed throughout the seasons for V. mimicus. The organism was isolated from Bangladesh environments throughout the year, whereas it was not isolated in Okayama when the water temperature fell below 10 degrees C. Samples with as many as 9.0 x 10(2) CFU of V. mimicus per 100 ml of water in Dhaka and 1.5 x 10(4) CFU of V. mimicus per 100 ml of water in Okayama were detected during the study period. V. mimicus was not found in any environment with an average salinity of 10% or more. Brackish environments with an average salinity of 4% were observed to be the optimal natural condition for the pathogen. Using the API 20E system with the conventional test methods, we observed variations in biochemical properties within the V. mimicus species. This study reveals the inefficacy of the API 20E system to identify a significant percentage of V. mimicus. Therefore, in addition to the API 20E system, a salt tolerance test and a string test are recommended for identification of this species. Susceptibility testing of strains isolated from Okayama environments showed higher resistance to ampicillin and susceptibility to trimethoprim-sulfamethoxazole when compared with environmental isolates of V. mimicus from Bangladesh.     

Survival of enterococcal species in aquatic environments

Analysis of the survival ability of faecal streptococci/enterococci in the environment has almost invariably been conducted using the standard culture method (CFU counts) despite the demonstration that these microorganisms are capable of entering a viable but nonculturable (VBNC) state. In this study we evaluated the fate, in terms of culturability and viability, of different enterococcal species under laboratory stress conditions mimicking those of the aquatic environment. The results indicate that enterococcal species may activate two different survival strategies, namely starvation and the VBNC state, depending on the specific environmental condition. Moreover, the different enterococcal species can be divided into three groups on the basis of the time needed to activate the VBNC state and the resuscitation capability. The differences in activation of the two survival strategies and the different kinetics observed among the enterococcal species reaching the VBNC state should be taken into consideration when the microbiological quality of waters has to be evaluated and because of their role as faecal contamination indicators.     

Significance of bacterial ectoenzymes in aquatic environments

The report presents studies on temporal and spatial variations of kinetics (Vmax and Km) of bacterial ectoenzyme activity (-glucosidase - Glc, leucine aminopeptidase - Leu-amp) in the naturally eutrophic Plusee. Glc and Leu-amp activity were positively correlated with the flux of polymeric materials (polysaccharides, proteins) in the lake. Glc activity was low when algal populations grew actively, but during the algal bloom breakdown Glc activity increased rapidly. Leu-amp displayed the highest rates of activity in the epilimnion and was tightly coupled to bacterial production. The synthesis of studied ectoenzymes was under control of a repression/derepression mechanism. The significance of ectoenzymes for the transformation and bacterial utilization of organic matter, and their role in the microbial loop in aquatic environments is discussed.     

Sequestered organelles sustain aerobic microbial life in anoxic environments

We report aerobic eukaryotic microbial life in the dimly lit anoxic water layer of a small freshwater lake. The microbial eukaryote is the ciliated protozoon Histiobalantium natans . Electron microscopy of thin sections shows that the cytoplasm of the ciliate harbours sequestered chloroplasts and sequestered mitochondria. The sequestered chloroplasts are attached or in very close proximity to the ciliate's own mitochondria. The sequestered mitochondria also seem to be associated with host-ciliate mitochondria. We suggest that the oxygenic photosynthetic activity of sequestered chloroplasts, perhaps enhanced by respiration in sequestered mitochondria, contributes to servicing the respiratory oxygen requirements of the ciliate host in its anoxic habitat. Our observations are novel, with the discovery of an aerobic microbial eukaryote capable of thriving and completing its life cycle in an anoxic environment, fuelled by oxygen generated by sequestered chloroplasts. The acknowledged flexibility and functional diversity within eukaryotic microbial communities still have many secrets to release.