Microbial diversity in ikaite tufa columns: an alkaline,cold ecological niche in Greenland

Ikaite tufa columns from the Ikka Fjord in south-western Greenland constitute a natural, stable environment at low temperature and with a pH ranging from neutral at the exterior to very alkaline (pH 10.4) at the interior of the column. Phylogenetic analysis of culturable organisms revealed ten different isolates representing three of the major bacterial divisions. Nine of the isolates showed 94-99% similarity to known sequences, whereas one isolate displayed a low degree of similarity (less than 90%) to a Cyclobacterium species. Seven of the isolates were shown to be cold active alkaliphiles, whereas three isolates showed optimal growth at neutral pH. Phylogenetic analysis of DNA isolated directly from the ikaite material demonstrated the presence of a microbial flora more diverse than the culturable isolates. Whereas approximately half of the phylotypes showed 90-99% similarity to known meso- or thermophilic alkaliphiles, the rest of the sequences displayed less than 90% similarity when compared to known 16S rRNA gene sequences in databases. Thus, in the present paper, we demonstrate that ikaite columns that host a specialized macroscopic flora and fauna also contain a unique, cold active, alkaliphilic microflora.     

Bacterial diversity in permanently cold and alkaline ikaite columns from Greenland

Bacterial diversity in alkaline (pH 10.4) and permanently cold (4°C) ikaite tufa columns from the Ikka Fjord, SW Greenland, was investigated using growth characterization of cultured bacterial isolates with Terminal-restriction fragment length polymorphism (T-RFLP) and sequence analysis of bacterial 16S rRNA gene fragments. More than 200 bacterial isolates were characterized with respect to pH and temperature tolerance, and it was shown that the majority were cold-active alkaliphiles. T-RFLP analysis revealed distinct bacterial communities in different fractions of three ikaite columns, and, along with sequence analysis, it showed the presence of rich and diverse bacterial communities. Rarefaction analysis showed that the 109 sequenced clones in the 16S rRNA gene library represented between 25 and 65% of the predicted species richness in the three ikaite columns investigated. Phylogenetic analysis of the 16S rRNA gene sequences revealed many sequences with similarity to alkaliphilic or psychrophilic bacteria, and showed that 33% of the cloned sequences and 33% of the cultured bacteria showed less than 97% sequence identity to known sequences in databases, and may therefore represent yet unknown species.     

Acid microenvironments in microbial biofilms of antarctic endolithic microecosystems

Antarctic endolithic microecosystems harbour distinct biofilms. The lithic substrate and the microorganisms comprising these films are intimately linked, leading to complex mineral-microbe interactions. Hence, the microhabitats and microenvironments of these microecosystems are not only determined by the physicochemical features of the lithic substrate, but are also conditioned by the biological components of these biofilms. The Antarctic biofilms analysed in this study are characterized by the presence of extracellular polymer substances and acid microenvironments in the proximity of the cells; cyanobacteria appearing as key components. On ultrastructural analysis, these endolithic cyanobacteria showed differences in sheath organization, probably related to their spatial position in the lithic substrate. It is proposed that in this type of ecosystem, biofilm structure could favour the formation of microsites with specific physicochemical conditions appropriate for the survival of microbial communities in this extreme environment.     

A new species of Chroomonas (Cryptophyceae) living inside the submarine ikaite columns in the Ikkafjord, Southwest Greenland, with remarks on its ultrastructure and ecology

A species of Chroomonas that forms blue-green patches in the ikaite columns in the Ikkafjord, SW-Greenland near Iviituut, has been investigated by means of electron microscopy. It has a conspicuous eyespot, two distinct adjacent refractile bodies and a large pyrenoid. The flagellar branch of the gullet is provided with a ligula. A comparison with previously investigated species shows that this combination of characters is unique, and accordingly the Chroomonas is described as a new species, C. ikaitensis . Further details of its ultrastructure and of its ecology are discussed.     

Holocene carbon burial by lakes in SW Greenland

The role of the Arctic in future global change processes is predicted to be important because of the large carbon (C) stocks contained in frozen soils and peatlands. Lakes are an important component of arctic landscapes although their role in storing C is not well prescribed. The area around Kangerlussuaq, SW Greenland (66–68°N, 49–54°W) has extremely high lake density, with ∼20 000 lakes that cover about 14% of the land area. C accumulation rates and standing stock (kg C m⁻²), representing late- to mid-Holocene C burial, were calculated from AMS ¹⁴C-dated sediment cores from 11 lakes. Lake ages range from ∼10 000 cal yr  bp to ∼5400 cal yr  bp , and reflect the withdrawal of the ice sheet from west to east. Total standing stock of C accumulated in the studied lakes for the last ∼8000 years ranged from 28 to 71 kg C m⁻², (mean: ∼42 kg C m⁻²). These standing stock determinations yield organic C accumulation rates of 3.5–11.5 g C m⁻² yr⁻¹ (mean: ∼6 g C m⁻² yr⁻¹) for the last 4500 years. Mean C accumulation rates are not different for the periods 8–4.5 and 4.5–0 ka, despite cooling trends associated with the neoglacial period after 4.5 ka. We used the mean C standing stock to estimate the total C pool in small lakes (<100 ha) of the Kangerlussuaq region to be ∼4.9 × 10¹³ g C. This C stock is about half of that estimated for the soil pool in this region (but in 5% of the land area) and indicates the importance of incorporating lakes into models of regional C balance at high latitudes.     

The Villaviciosa tufa: a scale model for an active cool water tufa system,Guadalajara (Spain)

The Villaviciosa tufa building, on the banks of the Tajuña River, central Spain, is a recent perched springline tufa with four architectural elements: cascades, pools, channels, and barrages. The facies of the tufa building are LMC (low magnesium calcite) framestones of bryophytes, hanging stems, charophytes, phytoclastic rudstones, and rudstones of oncoids. Isotopic analyses give δ¹³C values ranging from ? 8.05 to ? 10.3‰ VPDB, and δ¹⁸O values from ? 6.9 to ? 7.45‰ VPDB. These values are in the range of most common tufa systems and such a short range of values is consistent with the Villaviciosa tufa building’s reduced dimensions. The mechanisms involved in precipitation vary within the building’s different environments, as reflected in the isotopic composition of the samples. Non-biogenic degassing values in cascade deposits (framestones of bryophytes) are the heaviest, whereas in pools, dominated by biogenic degassing, values for framestones of charophytes and phytoclasts are the lightest. Microbial bio-mediation is also strongly influenced by the development of oncoid, stromatolite, and bryophyte framestones. Temperature variation throughout the system of approximately 3 °C is not clearly reflected in the isotope signals. In short, in spite of the reduced dimensions of this tufa deposit, its notable environmental, facies, and geochemical variations may aid not only in the interpretation of detail of other tufa systems but also in the discussion of detailed facies analyses in paleoclimatic interpretations of this type of deposits.     

Establishment of endolithic populations of extremophilic Cyanidiales (Rhodophyta)

Background  

Cyanidiales are unicellular extremophilic red algae that inhabit acidic and high temperature sites around hot springs and have also adapted to life in endolithic and interlithic habitats. Comparative genomic analysis of Cyanidioschyzon merolae and Galdieria sulphuraria predicts that the latter may be more broadly distributed in extreme environments because its genome contains membrane transporters involved in the uptake of reduced carbon compounds that are absent from C. merolae. Analysis of an endolithic site in the Phlegrean Fields near Naples, Italy is consistent with this prediction showing this population to be comprised solely of the newly described lineage Galdieria -B and C. merolae to be limited to humid habitats. Here, we conducted an environmental PCR survey of another extreme environment in Tuscany, Italy and contrasted Cyanidiales population structure at endolithic and interlithic habitats in Naples and Tuscany.     

Shedding light on biogas: Phototrophic biofilms in anaerobic digesters hold potential for improved biogas production

Conventional anaerobic digesters intended for the production of biogas usually operate in complete darkness. Therefore, little is known about the effect of light on their microbial communities. In the present work, 16S rRNA gene amplicon Nanopore sequencing and shotgun metagenomic sequencing were used to study the taxonomic and functional structure of the microbial community forming a biofilm on the inner wall of a laboratory-scale transparent anaerobic biodigester illuminated with natural sunlight. The biofilm was composed of microorganisms involved in the four metabolic processes needed for biogas production, and it was surprisingly rich in Rhodopseudomonas faecalis, a versatile bacterium able to carry out photoautotrophic metabolism when grown under anaerobic conditions. The results suggested that this bacterium, which is able to fix carbon dioxide, could be considered for use in transparent biogas fermenters in order to contribute to the production of optimized biogas with a higher CH₄:CO₂ ratio than the biogas produced in regular, opaque digesters. To the best of our knowledge, this is the first study characterising the phototrophic biofilm associated with illuminated bioreactors.     

Macrobenthic species composition and diversity in the Godthaabsfjord system, SW Greenland

The southwest Greenland coast is made up of large and deep sill fjords. On the shelf, a number of shallow banks separated by deep troughs are located 20–50 km from the coast. We collected three 0.1-m² van Veen grabs at nine stations along a transect spanning from the inner Godthaabsfjord influenced by glaciers, across the shallow Fyllas Bank and out to the slope of the continental shelf at approximately 1,000 m depth. Along this transect, we explored patterns of macrobenthic diversity, species composition, abundance and biomass. The sampled stations were very different in terms of environmental variables, resulting in large differences in species composition primarily related to differences in depth, silt–clay fraction and chl a content of the sediment (BIO-ENV analysis). Habitat differences also reduced species spatial ranges and the majority of species were found at only one (49%) or two (20%) stations and, consequently, species turnover or beta diversity was high and correlated to differences in depth, silt–clay fraction and median sediment grain size. Species richness and diversity were lowest in sites exposed to sediment disturbance: near the glaciers in the inner fjord (physical disturbance by mineral sedimentation) and at selected stations on the shelf (bioturbation by burrowing sand eel). Alpha diversity and richness were only weakly correlated to environmental parameters, indicating that alpha richness and diversity are influenced by several factors or that relationships are non-linear as was found for species richness and silt–clay fraction.     

Distribution and feeding ecology of the Greenland shark (Somniosus microcephalus) in Greenland waters

Greenland sharks are widely distributed and most likely a highly abundant predator in arctic waters. Greenland sharks have previously been considered scavengers, but recent studies suggest that Greenland sharks also predate on live prey. In this study, distribution and feeding ecology in Greenland waters were investigated. Based on data from 25 years of surveys, Greenland sharks were usually caught at 400–700 m but were found at all depths between 100 and 1,200 m. Based on examination of stomachs from 30 Greenland sharks (total length of 258–460 cm), the most important prey items were Atlantic cod (65.6 % IRI), harp seal (9.9 % IRI), skates (5.2 % IRI) and wolffish (4.4 % IRI), but large geographical variations were observed. Prey composition and qualitative observations support the hypothesis of active predation. Consistent with other studies, the results of this work support the notion that the Greenland shark is an apex predator with the potential to influence trophic dynamics in the Arctic.     

Development of bacterial biofilms on artificial corals in comparison to surface-associated microbes of hard corals

Numerous studies have demonstrated the differences in bacterial communities associated with corals versus those in their surrounding environment. However, these environmental samples often represent vastly different microbial micro-environments with few studies having looked at the settlement and growth of bacteria on surfaces similar to corals. As a result, it is difficult to determine which bacteria are associated specifically with coral tissue surfaces. In this study, early stages of passive settlement from the water column to artificial coral surfaces (formation of a biofilm) were assessed. Changes in bacterial diversity (16S rRNA gene), were studied on artificially created resin nubbins that were modelled from the skeleton of the reef building coral Acropora muricata. These models were dip-coated in sterile agar, mounted in situ on the reef and followed over time to monitor bacterial community succession. The bacterial community forming the biofilms remained significantly different (R = 0.864 p<0.05) from that of the water column and from the surface mucus layer (SML) of the coral at all times from 30 min to 96 h. The water column was dominated by members of the α-proteobacteria, the developed community on the biofilms dominated by γ-proteobacteria, whereas that within the SML was composed of a more diverse array of groups. Bacterial communities present within the SML do not appear to arise from passive settlement from the water column, but instead appear to have become established through a selection process. This selection process was shown to be dependent on some aspects of the physico-chemical structure of the settlement surface, since agar-coated slides showed distinct communities to coral-shaped surfaces. However, no significant differences were found between different surface coatings, including plain agar and agar enhanced with coral mucus exudates. Therefore future work should consider physico-chemical surface properties as factors governing change in microbial diversity.     

Recent sightings of the bowhead whale (Balaena mysticetus) in Northeast Greenland and the Greenland Sea

By the end of the 19th century, European whalers had brought the bowhead whale (Balaena mysticetus) in the “Spitsbergen stock” ranging the waters between eastern Greenland and the western Russian Arctic to the verge of extinction. This paper presents observations of this species in Northeast Greenland and in the Greenland Sea between 1940 and 2004. The number of observations has increased in Northeast Greenland since the mid-1980s. Only three observations are known for the period 1940–1979 but during the 1980s, the 1990s and between 2000 and 2004, six, six and eight observations of bowhead whales were made, involving an absolute minimum of three, five and eight to ten different individuals, respectively. It remains uncertain whether this represents an increase in survey effort, an immigration from other areas, a recent recovery of an eastern Greenland relict “tribe” belonging to the Spitsbergen stock, or a combination of these factors.     

Opaque cells signal white cells to form biofilms in Candida albicans

Upon homozygosis from a/alpha to a/a or alpha/alpha, Candida albicans must still switch from the 'white' to 'opaque' phenotype to mate. It was, therefore, surprising to discover that pheromone selectively upregulated mating-associated genes in mating-incompetent white cells without causing G1 arrest or shmoo formation. White cells, like opaque cells, possess pheromone receptors, although their distribution and redistribution upon pheromone treatment differ between the two cell types. In speculating about the possible role of the white cell pheromone response, it is hypothesized that in overlapping white a/a and alpha/alpha populations in nature, rare opaque cells, through the release of pheromone, signal majority white cells of opposite mating type to form a biofilm that facilitates mating. In support of this hypothesis, it is demonstrated that pheromone induces cohesiveness between white cells, minority opaque cells increase two-fold the thickness of majority white cell biofilms, and majority white cell biofilms facilitate minority opaque cell chemotropism. These results reveal a novel form of communication between switch phenotypes, analogous to the inductive events during embryogenesis in higher eukaryotes.     

Fluvival tufa formation in a hard-water creek (Deinschwanger Bach, Franconian Alb, Germany)

Summary Cyanobacteria-dominated biofilms involved in tufa deposition in the hardwater creek Deinschwanger Bach, Bavaria, were investigated with regard to their effect on the carbonate equilibrium and fabric formation. Current tufa deposition is evident by up to 1.5 mm thick crusts that have formed on substrate plates placed in the creek for 10 months. Hydrochemistry data indicate that carbonate precipitation along the creek is physicochemically driven by CO₂ degassing, whereas photosynthetic carbon assimilation is without detectable effect on the macroscale carbonate equilibrium. However, stable isotope data indicate a minor photosynthetic effect, but only for the lower creek section where the pCO₂ already drops to the two-fold of the atmospheric level. Though the initial process of external nucleation on cyanobacterial sheaths in the lower creck section might be promoted of by a photosynthetically-induced microscale pH gradient, the effect is not strong enough to cause a CaCO₃ impregnation of the sheaths. The fabric of the laminated tufa crusts in the creek reflects the temporal alternation of porous microspariticPhormidium incrustatum-Phormidium foveolarum-diatom biofilms in spring, micrite-impregnatedPhormidium incrustatum-Phormidium foveolarum-diatom biofilms in summerautumn, and detritus-rich non-calcified diatom-biofilms in winter. By contrast, exopolymer-poor surfaces of cascade tufa mosses show large, euhedral spar crystals. Non-phototrophic bacteria, which occur in large numbers inPhormidium incrustatum-Phormidium foveolarums-diatom-communities, thrive on extracellular polymeric substances (EPS) and dead cells of the cyanobacteria and are unlikely to promote CaCO₃ precipitation.     

Polyamine metabolism in primary human colon adenocarcinoma cells (SW480) and their lymph node metastatic derivatives (SW620)

The natural polyamines are multifunctional constituents of all eucaryotic cells. The objective of this work was to compare aspects of polyamine metabolism in two related cell lines with the idea to investigate whether metabolic differences can be attributed to functional differences of the cells. The human colon carcinoma-derived cell lines SW480 and SW620 were chosen as models. SW480 cells were isolated from the primary tumour, SW620 cells from a lymph node of the same patient. SW620 cells grow faster, and the key regulatory enzymes of polyamine biosynthesis (ODC and AdoMetDC) are more active in the metastatic cells. Moreover, their ability to accumulate polyamines from the environment is more important than of SW480 cells. Likewise polyamine concentrations were markedly higher in SW620 cells, although they are much smaller than SW480 cells, and have a particularly small cytoplasmic space. Both cell lines show a striking diminution of ODC and AdoMetDC activities and changes in the polyamine patterns at the transition from exponential to non-exponential growth--most probably as a consequence of high cell density. Depletion of putrescine and spermidine due to inactivation of ODC by DFMO causes accumulation of cells in G1, and a proportional decrease of S-phase cells in both cell lines. Based on morphologic and other criteria SW480 and SW620 cells were typified as poorly differentiated. In agreement with their low grade of differentiation they exhibit a low alkaline phosphatase activity. However, the time-dependent decrease of alkaline phosphatase is not typical of differentiation patterns of other adenocarcinoma-derived cell lines or of normal enterocytes. The high capacity of de novo polyamine biosynthesis and of polyamine uptake is presumably a prerequisite for the rapid growth and invasiveness. The fact that these properties were more accentuated in the case of SW620 cells and paralleled enhanced metastatic properties indicate relationships between basic parameters of polyamine metabolism and malignancy.     

Biomineralization of endolithic microbes in rocks from the McMurdo Dry Valleys of Antarctica: implications for microbial fossil formation and their detection

In some zones of Antarctica's cold and dry desert, the extinction of cryptoendolithic microorganisms leaves behind inorganic traces of microbial life. In this paper, we examine the transition from live microorganisms, through their decay, to microbial fossils using in situ microscopy (transmission electron microscopy, scanning electron microscopy in back-scattered electron mode) and microanalytical (energy dispersive X-ray spectroscopy) techniques. Our results demonstrate that, after their death, endolithic microorganisms inhabiting Commonwealth Glacier sandstone from the Antarctica McMurdo Dry Valleys become mineralized. In some cases, epicellular deposition of minerals and/or simply filling up of empty moulds by minerals leads to the formation of cell-shaped structures that may be considered biomarkers. The continuous deposition of allochthonous clay minerals and sulfate-rich salts fills the sandstone pores. This process can give rise to microbial fossils with distinguishable cell wall structures. Often, fossilized cell interiors were of a different chemical composition to the mineralized cell walls. We propose that the microbial fossil formation observed was induced by mineral precipitation resulting from inorganic processes occurring after the death of cryptoendolithic microorganisms. Nevertheless, it must have been the organic template that provoked the diffusion of mineral elements and gave rise to their characteristic distribution pattern inside the fossilized cells.     

Functional phenotypic plasticity of the endolithic mytilid Leiosolenus curtus (Lischke, 1874) (Bivalvia: Mytilidae)

In Sagami Bay, Japan, Leiosolenus curtus (Lischke, 1874) bores into dead shells of rock barnacles (Tetraclita japonica) in Manazuru, calcareous sand-rock in Oiso, weathered tuff in Miura and agglomerates formed by the tubes of clam worms (Spirobranchus kraussii) in Kanaya. In order to understand the relationships between morphology and environment, the shell morphologies and genetic characteristics of L. curtus, together with the calcium content of the different bored substrata, were analysed. Individuals from Kanaya and Manazuru were characterised by a chalk-like encrustation and a more rounded and inflated shell shape, while those from Oiso and Miura had a striated encrustation. The molecular phylogenetic tree and haplotype network showed that the genetic sequences of the individuals from all investigated localities were very similar, and implied that they belong to the same species. The striated encrustation of the individuals from Oiso and Miura presumably enables them to scrape those residues not dissolved by the mucus secreted by the mantle gland, and thereby to bore into non-calcareous substrata. The more rounded and inflated shell shape of the individuals from Manazuru is thought to be advantageous for boring into thin substrata.     

Phototrophic Fe(II) oxidation by Rhodopseudomonas palustris TIE-1 in organic and Fe(II)-rich conditions

Rhodopseudomonas palustris TIE-1 grows photoautotrophically with Fe(II) as an electron donor and photoheterotrophically with a variety of organic substrates. However, it is unclear whether R. palustris TIE-1 conducts Fe(II) oxidation in conditions where organic substrates and Fe(II) are available simultaneously. In addition, the effect of organic co-substrates on Fe(II) oxidation rates or the identity of Fe(III) minerals formed is unknown. We incubated R. palustris TIE-1 with 2 mM Fe(II), amended with 0.6 mM organic co-substrate, and in the presence/absence of CO₂. We found that in the absence of CO₂, only the organic co-substrates acetate, lactate and pyruvate, but not Fe(II), were consumed. When CO₂ was present, Fe(II) and all organic substrates were consumed. Acetate, butyrate and pyruvate were consumed before Fe(II) oxidation commenced, whereas lactate and glucose were consumed at the same time as Fe(II) oxidation proceeded. Lactate, pyruvate and glucose increased the Fe(II) oxidation rate significantly (by up to threefold in the case of lactate). ⁵⁷Fe Mössbauer spectroscopy revealed that short-range ordered Fe(III) oxyhydroxides were formed under all conditions. This study demonstrates phototrophic Fe(II) oxidation proceeds even in the presence of organic compounds, and that the simultaneous oxidation of organic substrates can stimulate Fe(II) oxidation.