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Actinobacteria – an ancient phylum active in volcanic rock weathering
Geomicrobiology Journal, 2013
A molecular biological analysis of Icelandic volcanic rocks of different compositions and glassiness revealed the presence of Actinobacteria as an abundant phylum. In outcrops of basaltic glass they were the dominant bacterial phylum. A diversity of Actinobacteria were cultured from the rocks on rock-agar plates showing that they are capable of growing on rock-derived nutrient sources and that many of the taxa identified by molecular methods are viable, potentially active members of the community. Laboratory batch-culture experiments using a Streptomyces isolate showed that it was capable of enhancing the release of major elements from volcanic rocks, including weathered basaltic glass, crystalline basalt and komatiite, when provided with a carbon source. Actinobacteria of a variety of other sub-orders were also capable of enhancing volcanic rock weathering, measured as Si release. However, most strains did not significantly increase the weathering of the silica-rich rock, obsidian. These data show that Actinobacteria can contribute to volcanic rock weathering and, therefore, the carbonate-silicate cycle. Given their ancient lineage, it is likely they have played a role in rock weathering for over two billion years.
Actinobacteria paper final version accepted
2013
A molecular biological analysis of Icelandic volcanic rocks of different compositions and glassiness revealed the presence of Actinobacteria as an abundant phylum. In outcrops of basaltic glass they were the dominant bacterial phylum. A diversity of Actinobacteria were cultured from the rocks on rock-agar plates showing that they are capable of growing on rock-derived nutrient sources and that many of the taxa identified by molecular methods are viable, potentially active members of the community. Laboratory batch-culture experiments using a Streptomyces isolate showed that it was capable of enhancing the release of major elements from volcanic rocks, including weathered basaltic glass, crystalline basalt and komatiite, when provided with a carbon source. Actinobacteria of a variety of other suborders were also capable of enhancing volcanic rock weathering, measured as Si release.
Bacteria in weathered basaltic glass, Iceland
Geomicrobiology …, 2009
Bacteria play an important role in rock weathering and yet their diversity and potential activity in the terrestrial rock weathering environment is poorly understood. Culture and culture-independent methods (16S rDNA) were used to investigate the populations of bacteria inhabiting a basaltic glass/palagonite subglacial (hyaloclastite) deposit subject to weathering in Iceland. The rock hosts a diverse microbial community. The 16S rDNA clones were dominated by Actinobacteria, Proteobacteria, Bacteroidetes and Acidobacteria. Representatives of Gemmatimonadetes and Verrucomicrobia were present. Isolation of organisms on basalt/palagonite yielded only two isolates, an actinobacterium and a Bacteroidetes, showing that the active species, at least in the time scale of laboratory cultivation, are a small proportion of the total diversity. Firmicutes and Actinobacteria were isolated when basalt/palagonite was supplemented with an organic source. Many of the isolates demonstrated tolerance to transition metals (Cr, Cu, Zn, Ni, Co) naturally present in the rock. The growth of the isolates was inhibited at typical pH values for Icelandic rain, which suggests that the increase in pH caused by the consumption of protons in rock weathering, for example by palagonite formation, may play a role in defining which organisms are active. Colonization experiments show that the filamentous growth habit of the actinobacterium isolated on basalt/palagonite allows it to actively invade and colonise the basaltic glass. The filamentous growth of some actinobacteria may be an important contributor to their role in systemic interstitial rock weathering in the natural environment.
Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions
Frontiers in Microbiology, 2015
Volcanic caves are filled with colorful microbial mats on the walls and ceilings. These volcanic caves are found worldwide, and studies are finding vast bacteria diversity within these caves. One group of bacteria that can be abundant in volcanic caves, as well as other caves, is Actinobacteria. As Actinobacteria are valued for their ability to produce a variety of secondary metabolites, rare and novel Actinobacteria are being sought in underexplored environments. The abundance of novel Actinobacteria in volcanic caves makes this environment an excellent location to study these bacteria. Scanning electron microscopy (SEM) from several volcanic caves worldwide revealed diversity in the morphologies present. Spores, coccoid, and filamentous cells, many with hair-like or knobby extensions, were some of the microbial structures observed within the microbial mat samples. In addition, the SEM study pointed out that these features figure prominently in both constructive and destructive mineral processes. To further investigate this diversity, we conducted both Sanger sequencing and 454 pyrosequencing of the Actinobacteria in volcanic caves from four locations, two islands in the Azores, Portugal, and Hawai`i and New Mexico, USA. This comparison represents one of the largest sequencing efforts of Actinobacteria in volcanic caves to date. The diversity was shown to be dominated by Actinomycetales, but also included several newly described orders, such as Euzebyales, and Gaiellales. Sixty-two percent of the clones from the four locations shared less than 97% similarity to known sequences, and nearly 71% of the clones were singletons, supporting the commonly held belief that volcanic caves are an untapped resource for novel and rare Actinobacteria. The amplicon libraries depicted a wider view of the microbial diversity in Azorean volcanic caves revealing three additional orders, Rubrobacterales, Solirubrobacterales, and Coriobacteriales. Studies of microbial ecology in volcanic caves are still very limited. To rectify this deficiency, the results from our study help fill in the gaps in our knowledge of actinobacterial diversity and their potential roles in the volcanic cave ecosystems.
Biotechnological potential of Actinobacteria from Canadian and Azorean volcanic caves
Applied Microbiology and Biotechnology, 2016
Caves are regarded as extreme habitats with appropriate conditions for the development of Actinobacteria. In comparison with other habitats, caves have not yet been the target of intensive screening for bioactive secondary metabolites produced by actinomycetes. As a primary screening strategy, we conducted a metagenomic analysis of the diversity and richness of a key gene required for non-ribosomal peptide (NRP) biosynthesis, focusing on cave-derived sediments from two Canadian caves (a lava tube and a limestone cave) to help us predict whether different types of caves may harbor drugproducing actinobacteria. Using degenerate PCR primers targeting adenylation domains (AD), a conserved domain in the core gene in NRP biosynthesis, a number of amplicons were obtained that mapped back to biomedically relevant NRP gene cluster families. This result guided our culturedependent sampling strategy of actinomycete isolation from the volcanic caves of Canada (British Columbia) and Portugal (Azores) and subsequent characterization of their antibacterial and enzymatic activities. Multiple enzymatic and antimicrobial activities were identified from bacterial of the Arthrobacter and Streptomyces genera demonstrating that actinomycetes from volcanic caves are promising sources of antibacterial, antibiofilm compounds and industrially relevant enzymes.
The biogeochemical role of Actinobacteria in Altamira Cave, Spain
FEMS Microbiology Ecology, 2012
The walls and ceiling of Altamira Cave, northern Spain, are coated with different coloured spots (yellow, white and grey). Electron microscopy revealed that the grey spots are composed of bacteria and bioinduced CaCO 3 crystals. The morphology of the spots revealed a dense network of microorganisms organized in well-defined radial and dendritic divergent branches from the central area towards the exterior of the spot, which is coated with overlying spheroidal elements of CaCO 3 and CaCO 3 nest-like aggregates. Molecular analysis indicated that the grey spots were mainly formed by an unrecognized species of the genus Actinobacteria. CO 2 efflux measurements in rocks heavily covered by grey spots confirmed that bacteria-forming spots promoted uptake of the gas, which is abundant in the cave. The bacteria can use the captured CO 2 to dissolve the rock and subsequently generate crystals of CaCO 3 in periods of lower humidity and/or CO 2. A tentative model for the formation of these grey spots, supported by scanning electron microscopy and transmission electron microscopy data, is proposed.
High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits
Antibiotics (Basel, Switzerland), 2018
Moonmilk are cave carbonate deposits that host a rich microbiome, including antibiotic-producing Actinobacteria, making these speleothems appealing for bioprospecting. Here, we investigated the taxonomic profile of the actinobacterial community of three moonmilk deposits of the cave "Grotte des Collemboles" via high-throughput sequencing of 16S rRNA amplicons. Actinobacteria was the most common phylum after Proteobacteria, ranging from 9% to 23% of the total bacterial population. Next to actinobacterial operational taxonomic units (OTUs) attributed to uncultured organisms at the genus level (~44%), we identified 47 actinobacterial genera with (4 OTUs, 17%) and (9 OTUs, ~16%) as the most abundant in terms of the absolute number of sequences. Streptomycetes presented the highest diversity (19 OTUs, 3%), with most of the OTUs unlinked to the culturable strains that were previously isolated from the same deposits. Furthermore, 43% of the OTUs were shared between the three stud...
AFRICAN JOURNAL OF BIOTECHNOLOGY, 2011
A phosphate mine from Togo, an original biotope rich in insoluble rock phosphate (RP), was explored for the presence of RP solubilizing actinobacteria. One hundred and fifty actinobacteria isolates originating from this mine was tested for their ability to grow on a synthetic minimum medium (SMM) containing insoluble RP as unique phosphate source. Only 29 isolates (19%) were able to weather RP in SMM medium. Five isolates showed the most active growth and solubilization capability. These isolates were shown to be able to solubilize RP in liquid cultures. The study of mechanisms involved in these weathering processes indicated that the isolates produce siderophores but not organic acids. Four of these strains were shown to belong to the genus Micromonospora and one, to the genus Streptomyces.
Scientific reports, 2018
Microbial diversity in lava tubes from Canary Islands (Spain) has never been explored thus far offering a unique opportunity to study subsurface microbiology. Abundant yellow coloured mats developing on coralloid speleothems in a lava tube from La Palma Islands were studied by next-generation sequencing and DNA/RNA clone library analyses for investigating both total and metabolically active bacteria. In addition, morphological and mineralogical characterization was performed by field emission scanning electron microscopy (FESEM), micro-computed tomography, X-ray diffraction and infrared spectroscopy to contextualize sequence data. This approach showed that the coralloid speleothems consist of banded siliceous stalactites composed of opal-A and hydrated halloysite. Analytical pyrolysis was also conducted to infer the possible origin of cave wall pigmentation, revealing that lignin degradation compounds can contribute to speleothem colour. Our RNA-based study showed for the first time...
Microbial colonization of basaltic glasses in hydrothermal organic-rich sediments at Guaymas Basin
Frontiers in Microbiology, 2013
Oceanic basalts host diverse microbial communities with various metabolisms involved in C, N, S, and Fe biogeochemical cycles which may contribute to mineral and glass alteration processes at, and below the seafloor. In order to study the microbial colonization on basaltic glasses and their potential biotic/abiotic weathering products, two colonization modules called AISICS ("Autonomous in situ Instrumented Colonization System") were deployed in hydrothermal deep-sea sediments at the Guaymas Basin for 8 days and 22 days. Each AISICS module contained 18 colonizers (including sterile controls) filled with basaltic glasses of contrasting composition. Chemical analyses of ambient fluids sampled through the colonizers showed a greater contribution of hydrothermal fluids (maximum temperature 57.6 • C) for the module deployed during the longer time period. For each colonizer, the phylogenetic diversity and metabolic function of bacterial and archaeal communities were explored using a molecular approach by cloning and sequencing. Results showed large microbial diversity in all colonizers. The bacterial distribution was primarily linked to the deployment duration, as well as the depth for the short deployment time module. Some 16s rRNA sequences formed a new cluster of Epsilonproteobacteria. Within the Archaea the retrieved diversity could not be linked to either duration, depth or substrata. However, mcrA gene sequences belonging to the ANME-1 mcrA-guaymas cluster were found sometimes associated with their putative sulfate-reducers syntrophs depending on the colonizers. Although no specific glass alteration texture was identified, nano-crystals of barite and pyrite were observed in close association with organic matter, suggesting a possible biological mediation. This study gives new insights into the colonization steps of volcanic rock substrates and the capability of microbial communities to exploit new environmental conditions.
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Bacterial Diversity of Terrestrial Crystalline Volcanic Rocks, Iceland
Microbial Ecology, 2011
Bacteria inhabiting crystalline rocks from two terrestrial Icelandic volcanic lava flows of similar age and from the same geographical region, but differing in porosity and mineralogy, were characterised. Microarray (PhyloChip) and clone library analysis of 16S rRNA genes revealed the presence of a diverse assemblage of bacteria in each lava flow. Both methods suggested a more diverse community at the Dómadalshraun site (rhyolitic/andesitic lava flow) than that present at the Hnausahraun site (basaltic lava flow). Proteobacteria dominated the clone library at the Dómadalshraun site, while Acidobacteria was the most abundant phylum in the Hnausahraun site. Although analysis of similarities of denaturing gradient gel electrophoresis profiles suggested a strong correlation of community structure with mineralogy, rock porosity may also play an important role in shaping the bacterial community in crystalline volcanic rocks. Clone sequences were most similar to uncultured microorganisms, mainly from soil environments. Of these, Antarctic soils and temperate rhizosphere soils were prominent, as were clones retrieved from Hawaiian and Andean volcanic soils. The novel diversity of these Icelandic microbial communities was supported by the finding that up to 46% of clones displayed <85% sequence identities to sequences currently deposited in the RDP database.
Comparison of Bacterial Diversity in Azorean and Hawai'ian Lava Cave Microbial Mats
Geomicrobiology Journal, 2014
Worldwide, lava caves host colorful microbial mats. However, little is known about the diversity of these microorganisms, or what role they may play in the subsurface ecosystem. White and yellow microbial mats were collected from four lava caves each on the Azorean island of Terceira and the Big Island of Hawai'i, to compare the bacterial diversity found in lava caves from two widely separated archipelagos in two different oceans at different latitudes. Scanning electron microscopy of mat samples showed striking similarities between Terceira and Hawai'ian microbial morphologies. 16S rRNA gene clone libraries were constructed to determine the diversity within these lava caves. Fifteen bacterial phyla were found across the samples, with more Actinobacteria clones in Hawai'ian communities and greater numbers of Acidobacteria clones in Terceira communities. Bacterial diversity in the subsurface was correlated with a set of factors. Geographical location was the major contributor to differences in community composition (at the OTU level), together with differences in the amounts of organic carbon, nitrogen and copper available in the lava rock that forms the cave. These results reveal, for the first time, the similarity among the extensive bacterial diversity found in lava caves in two geographically separate locations and contribute to the current debate on the nature of microbial biogeography.
The effect of rock composition on cyanobacterial weathering of crystalline basalt and rhyolite
Geobiology, 2012
The weathering of volcanic rocks contributes significantly to the global silicate weathering budget, effecting carbon dioxide drawdown and long-term climate control. The rate of chemical weathering is influenced by the composition of the rock. Rock-dwelling micro-organisms are known to play a role in changing the rate of weathering reactions; however, the influence of rock composition on bio-weathering is unknown. Cyanobacteria are known to be a ubiquitous surface taxon in volcanic rocks. In this study, we used a selection of fast and slow growing cyanobacterial species to compare microbial-mediated weathering of bulk crystalline rocks of basaltic and rhyolitic composition, under batch conditions. Cyanobacterial growth caused an increase in the pH of the medium and an acceleration of rock dissolution compared to the abiotic controls. For example, Anabaena cylindrica increased the linear release rate (R l i ) of Ca, Mg, Si and K from the basalt by more than fivefold (5.21-12.48) and increased the pH of the medium by 1.9 units. Although A. cylindrica enhanced rhyolite weathering, the increase in R l i was less than threefold (2.04-2.97) and the pH increase was only 0.83 units. The R l i values obtained with A. cylindrica were at least ninefold greater with the basalt than the rhyolite, whereas in the abiotic controls, the difference was less than fivefold. Factors accounting for the slower rate of rhyolite weathering and lower biomass achieved are likely to include the higher content of quartz, which has a low rate of weathering and lower concentrations of bio-essential elements, such as, Ca, Fe and Mg, which are known to be important in controlling cyanobacterial growth. We show that at conditions where weathering is favoured, biota can enhance the difference between low and high Si-rock weathering. Our data show that cyanobacteria can play a significant role in enhancing rock weathering and likely have done since they evolved on the early Earth.
Actinobacteria —an ancient phylum active in volcanic rock weathering
Geomicrobiology Journal, 2013
A molecular biological analysis of Icelandic volcanic rocks of different compositions and glassiness revealed the presence of Actinobacteria as an abundant phylum. In outcrops of basaltic glass they were the dominant bacterial phylum. A diversity of Actinobacteria were cultured from the rocks on rock-agar plates showing that they are capable of growing on rock-derived nutrient sources and that many of the taxa identified by molecular methods are viable, potentially active members of the community. Laboratory batch-culture experiments using a Streptomyces isolate showed that it was capable of enhancing the release of major elements from volcanic rocks, including weathered basaltic glass, crystalline basalt and komatiite, when provided with a carbon source. Actinobacteria of a variety of other sub-orders were also capable of enhancing volcanic rock weathering, measured as Si release. However, most strains did not significantly increase the weathering of the silica-rich rock, obsidian. These data show that Actinobacteria can contribute to volcanic rock weathering and, therefore, the carbonate-silicate cycle. Given their ancient lineage, it is likely they have played a role in rock weathering for over two billion years.
BMC microbiology, 2018
Basalt is the most common igneous rock on the Earth's surface covering. Basalt-associated microorganisms drive the cycling and sequestration of different elements such as nitrogen, carbon and other nutrients, which facilitate subsequent pioneer and plant development, impacting long-term regulation of the Earth's temperature and biosphere. The initial processes of colonization and subsequent rock weathering by microbial communities are still poorly understood and relatively few data are available on the diversity and richness of the communities inhabiting successive and chronological lava flows. In this study, the bacterial communities present on lava deposits from different eruptions of the 1975-84 Krafla Fires (32-, 35- and 39-year old, respectively) at the Krafla, Iceland, were determined. Three sites were sampled for each deposit (32-, 35- and 39-year old), two proximal sites (at 10 m distance) and one more distant site (at 100 m from the two other sites). The determined ...
BioRock: new experiments and hardware to investigate microbe–mineral interactions in space
International Journal of Astrobiology
In this paper, we describe the development of an International Space Station experiment, BioRock. The purpose of this experiment is to investigate biofilm formation and microbe–mineral interactions in space. The latter research has application in areas as diverse as regolith amelioration and extraterrestrial mining. We describe the design of a prototype biomining reactor for use in space experimentation and investigations on in situ Resource Use and we describe the results of pre-flight tests.
Cryogenic Minerals in Hawaiian Lava Tubes: A Geochemical and Microbiological Exploration
Geomicrobiology Journal
Mauna Loa volcano, on the Island of Hawaii, has numerous young lava tube caves. Among them, two at high altitude are known to contain ice year-round: Mauna Loa Icecave and Arsia Cave. These unusual caves harbor cold, humid, dark, and biologically restricted environments. Secondary minerals and ice were sampled from both caves to explore their geochemical and microbiological characteristics. The minerals sampled from the deep parts of the caves, where near freezing temperatures prevail, are all multi-phase and consist mainly of secondary amorphous silica SiO 2 , cryptocrystalline calcite CaCO 3 , and gypsum CaSO 4 •2H 2 O. Based on carbon and oxygen stable isotope ratios, all sampled calcite is cryogenic.
Biogeosciences, 2015
Colonization of life on Surtsey has been observed systematically since the formation of the island 50 years ago. Although the first colonisers were prokaryotes, such as bacteria and blue-green algae, most studies have been focused on the settlement of plants and animals but less on microbial succession. To explore microbial colonization in diverse soils and the influence of associated vegetation and birds on numbers of environmental bacteria, we collected 45 samples from different soil types on the surface of the island. Total viable bacterial counts were performed with the plate count method at 22, 30 and 37 • C for all soil samples, and the amount of organic matter and nitrogen (N) was measured. Selected samples were also tested for coliforms, faecal coliforms and aerobic and anaerobic bacteria. The subsurface biosphere was investigated by collecting liquid subsurface samples from a 181 m borehole with a special sampler. Diversity analysis of uncultivated biota in samples was performed by 16S rRNA gene sequences analysis and cultivation. Correlation was observed between nutrient deficits and the number of microorganisms in surface soil samples. The lowest number of bacteria (1 × 10 4 − 1 × 10 5 cells g −1) was detected in almost pure pumice but the count was significantly higher (1 × 10 6 − 1 × 10 9 cells g −1) in vegetated soil or pumice with bird droppings. The number of faecal bacteria correlated also to the total number of bacteria and type of soil. Bacteria belonging to Enterobacteriaceae were only detected in vegetated samples and samples containing bird droppings. The human pathogens Salmonella, Campylobacter and Listeria were not in any sample. Both thermophilic bacteria and archaea 16S rDNA sequences were found in the subsurface samples collected at 145 and 172 m depth at 80 and 54 • C, respectively, but no growth was observed in enrichments. The microbiota sequences generally showed low affiliation to any known 16S rRNA gene sequences.
Space Science Reviews
With no large-scale granitic continental crust, all environments on Mars are fundamentally derived from basaltic sources or, in the case of environments such as ices, evaporitic, and sedimentary deposits, influenced by the composition of the volcanic crust. Therefore, the selection of samples on Mars by robots and humans for investigating habitability or testing for the presence of life should be guided by our understanding of the microbial ecology of volcanic terrains on the Earth. In this paper, we discuss the microbial ecology of volcanic rocks and hydrothermal systems on the Earth. We draw on microbiological investigations of volcanic environments accomplished both by microbiology-focused studies and Mars analog studies such as the NASA BASALT project. A synthesis of these data emphasises a number of common patterns that include: (1) the heterogeneous distribution of
Pioneer microbial communities of the Fimmvörðuháls lava flow, Eyjafjallajökull, Iceland
Microbial ecology, 2014
Little is understood regarding the phylogeny and metabolic capabilities of the earliest colonists of volcanic rocks, yet these data are essential for understanding how life becomes established in and interacts with the planetary crust, ultimately contributing to critical zone processes and soil formation. Here, we report the use of molecular and culture-dependent methods to determine the composition of pioneer microbial communities colonising the basaltic Fimmvörðuháls lava flow at Eyjafjallajökull, Iceland, formed in 2010. Our data show that 3 to 5 months post eruption, the lava was colonised by a low-diversity microbial community dominated by Betaproteobacteria, primarily taxa related to non-phototrophic diazotrophs such as Herbaspirillum spp. and chemolithotrophs such as Thiobacillus. Although successfully cultured following enrichment, phototrophs were not abundant members of the Fimmvörðuháls communities, as revealed by molecular analysis, and phototrophy is therefore not likel...
Frontiers in Astronomy and Space Sciences, 2020
Recent studies have uncovered a vast number of thermophilic species in icy environments, permanently cold ocean sediments, cold sea waters, and cool soils. The survival of thermophiles in psychrobiotic habitats requires thorough investigation of the physiological and molecular mechanisms behind their natural cryopreservation. Such investigations are mainly impeded due to a restricted cultivation of thermophiles at low temperatures under the laboratory conditions. Artificial culture media used under the laboratory conditions usually fail to support cultivation of thermophiles at low-temperature range. In this study we cultivated the extreme thermoacidophilic archaeon Metallosphaera sedula with the preliminary powdered and sterilized multimetallic extraterrestrial mineral material (the meteorite NWA 1172) under a low temperature regime in laboratory conditions. Our data indicate that M. sedula withstands cold stress and can be maintained at low temperatures, when supplemented with the meteorite NWA 1172 as the sole energy source. Cultivation with the meteorite NWA 1172 opens up new, previously unknown psychrotolerant characteristics of M. sedula, emphasizing that culture conditions (i.e., the "nutritional environment") may affect the microbial survival potential in stress related situations. These observations facilitate further investigation of strategies and underlying molecular mechanisms of the survival of thermophilic species in permanently cold habitats.
The bacterial diversity on steam vents from Paricutín and Sapichu volcanoes
Extremophiles, 2019
Vapor steam vents are prevailing structures on geothermal sites in which local geochemical conditions allow the development of extremophilic microorganisms. We describe the structure of the prokaryotic community able to grow on the walls and rocks of such microecosystems in two terrestrial Mexican volcanoes: Paricutín (PI and PII samples) and its satellite Sapichu (S sample). The investigated samples showed similar diversity indices, with few dominant OTUs (abundance > 1%): 21, 16 and 23, respectively for PI, PII and S. However, each steam vent showed a particular community profile: PI was dominated by photosynthetic bacteria (Cyanobacteria and Chloroflexia class), PII by Actinobacteria and Proteobacteria, and S by Ktedonobacteria class, Acidobacteria and Cyanobacteria phyla. Concerning the predicted metabolic potential, we found a dominance of cellular pathways, especially the ones for energy generation with metabolisms for sulfur respiration, nitrogen fixation, methanogenesis, carbon fixation, photosynthesis, and metals, among others. We suggest a different maturity stage for the three studied fumaroles, from the youngest (PI) to the oldest (S and PII), also influenced by the temperature and other geochemical parameters. Furthermore, four anaerobic strains were isolated, belonging to Clostridia class (Clostridium sphenoides, C. swellfunanium and Anaerocolumna cellulosilytica) and to Bacilli class (Paenibacillus azoreducens).
Minerals, 2020
Miocene tuffs preserved in argillaceous sediment interbedded with lacustrine successions are commonly encountered throughout the Dinarides Lake System (DLS) in south-eastern Europe. In this contribution the volcanic glass degradation and co-genetic Mn-Fe precipitation were studied in a 14.68 Ma felsic tuff from DLS Livno-Tomislavgrad Basin. Microbial activity has been involved in both reactions thus adding the interest of revealing effects of biotic and abiotic processes taking place during tuff eogenesis. X-ray diffraction and electron microbeam analysis with energy-dispersive X-ray spectroscopy revealed the pitting or granular structures developed at glass rims along with smectite flakes protruding from a degrading glass. Mn-Fe mineralization emerges in the form of Mn-Fe coatings, an initial step to micronodule formation, where traces of biogenetic influence included a high content of phases rich in structural Mn (IV) (i.e., ranciéite and jacobsite) and presence of microbial micro...
Current Microbiology, 2013
Alpha and beta diversities of the bacterial communities growing on rock surfaces, proto-soils, riparian sediments, lichen thalli, and water springs biofilms in a glacier foreland were studied. We used three molecular based techniques to allow a deeper investigation at different taxonomic resolutions: denaturing gradient gel electrophoresis, length heterogeneity-PCR, and automated ribosomal intergenic spacer analysis. Bacterial communities were mainly composed of Acidobacteria, Proteobacteria, and Cyanobacteria with distinct variations among sites. Proteobacteria were more represented in sediments, biofilms, and lichens; Acidobacteria were mostly found in proto-soils; and Cyanobacteria on rocks. Firmicutes and Bacteroidetes were mainly found in biofilms. UniFrac P values confirmed a significant difference among different matrices. Significant differences (P \ 0.001) in beta diversity were observed among the different matrices at the genus-species level, except for lichens and rocks which shared a more similar community structure, while at deep taxonomic resolution two distinct bacterial communities between lichens and rocks were found.
Volcanic ash supports a diverse bacterial community in a marine mesocosm
Geobiology, 2017
Shallow-water coral reef ecosystems, particularly those already impaired by anthropogenic pressures, may be highly sensitive to disturbances from natural catastrophic events, such as volcanic eruptions. Explosive volcanic eruptions expel large quantities of silicate ash particles into the atmosphere, which can disperse across millions of square kilometres and deposit into coral reef ecosystems. Following heavy ash deposition, mass mortality of reef biota is expected, but little is known about the recovery of post-burial reef ecosystems. Reef regeneration depends partly upon the capacity of the ash deposit to be colonised by waterborne bacterial communities and may be influenced to an unknown extent by the physiochemical properties of the ash substrate itself. To determine the potential for volcanic ash to support pioneer bacterial colonisation, we exposed five well-characterised volcanic and coral reef substrates to a marine aquarium under low light conditions for 3 months: volcanic ash, synthetic volcanic glass, carbonate reef sand, calcite sand and quartz sand. Multivariate statistical analysis of Automated Ribosomal Intergenic Spacer Analysis (ARISA) fingerprinting data demonstrates clear segregation of volcanic substrates from the quartz and coral reef substrates over 3 months of bacterial colonisation. Overall bacterial diversity showed shared and substrate-specific bacterial communities; however, the volcanic ash substrate supported the most diverse bacterial community. These data suggest a significant influence of substrate properties (composition, granulometry and colour) on bacterial settlement. Our findings provide first insights into physicochemical controls on pioneer bacterial colonisation of volcanic ash and highlight the potential for volcanic ash deposits to support bacterial diversity in the aftermath of reef burial, on timescales that could permit cascading effects on larval settlement. 1 | INTRODUCTION Coral reefs are unique, biodiverse ecosystems of high socioeconomic importance on both global and local scales (Nicholls et al., 2007). Anthropogenic disturbances, such as sedimentation and eutrophication, increasingly pressure fragile coral reef ecosystems worldwide (Wilkinson 1999). The deterioration of water quality in coastal regions consequently favours macro-algal dominance (Fabricius, 2005; Schaffelke, Mellors, & Duke, 2005) and increases the risk of disease for coral reef-building species, including sponges and corals (Haapkyla et al., 2011; Webster, Xavier, Freckelton, Motti, & Cobb, 2008), which further exacerbates coral reef vulnerability to catastrophic natural This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
Geomicrobiology Journal, 2020
Because microbes cannot be eliminated from radioactive waste disposal facilities, the consequences of bio-colonization must be understood. At a pre-Viking era vitrified hillfort, Broborg, Sweden, anthropogenic glass has been subjected to bio-colonization for over 1,500 years. Broborg is used as a habitat analogue for disposed radioactive waste glass to inform how microbial processes might influence long-term glass durability. Electron microscopy and DNA sequencing of surficial material from the Broborg vitrified wall, adjacent soil, and general topsoil show that the ancient glass supports a niche microbial community of bacteria, fungi, and protists potentially involved in glass alteration. Communities associated with the vitrified wall are distinct and less diverse than soil communities. The vitrified niche of the wall and adjacent soil are dominated by lichens, lichen-associated microbes, and other epilithic, endolithic, and epigeic organisms. These organisms exhibit potential bio-corrosive properties, including silicate dissolution, extraction of essential elements, and secretion of geochemically reactive organic acids, that could be detrimental to glass durability. However, long-term biofilms can also possess a homeostatic function that could limit glass alteration. This study documents potential impacts that microbial colonization and niche partitioning can have on glass alteration, and subsequent release of radionuclides from a disposal facility for vitrified radioactive waste.
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Diversity and adaptation properties of actinobacteria associated with Tunisian stone ruins
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Stone surface is a unique biological niche that may host a rich microbial diversity. The exploration of the biodiversity of the stone microbiome represents a major challenge and an opportunity to characterize new strains equipped with valuable biological activity. Here, we explored the diversity and adaptation strategies of total bacterial communities associated with Roman stone ruins in Tunisia by considering the effects of geo-climatic regions and stone geochemistry. Environmental 16S rRNA gene amplicon was performed on DNA extracted from stones samples collected in three different sampling sites in Tunisia, along an almost 400km aridity transect, encompassing Mediterranean, semiarid and arid climates. The library was sequenced on an Illumina MiSeq sequencing platform. The cultivable Actinobacteria were isolated from stones samples using the dilution plate technique. A total of 71 strains were isolated and identified based on 16S rRNA gene sequences. Cultivable actinobacteria were...
Journal of Scientific Research in Science
The search of novel strains continues to be of great importance in research around the world for pharmaceutical, industrial, agricultural and biomining applications. The present study aims to investigating the microbial diversity of rock samples collected from Um Bogma formation, southwestern Sinai, Egypt which was chosen for its unique location, geological and physicochemical properties. The studied samples showed small microbial diversity and low microbial count. A total of ten isolates of actinobacteria and ten isolates of fungi were isolated and characterized phenotypically. The results indicated that all the isolated actinobacteria belong to the genus Streptomyces. They were all halotolerant with some showing antimicrobial activities when tested against Bacillus subtilis, Pseudomonas aeruginosa ATCC 9027, Staphylococcus aureus ATCC 6538, Escherichia coli ATCC 8739, Candida albicans and Aspergillus flavus. On the other hand, all the studied fungal isolates belong to the genus Aspergillus. They showed resistance to the antifungal nystatin when a concentration of 50 µg per ml was used. The studied locations is characterized by their harsh conditions which does not support the growth of most microorganisms which includes a temperature ranging from below 0°C at night to above 46°C throughout the day, low water content and organic matter hosting radioactive and heavy elements. Rock-dwelling microbial communities that survived such conditions open further
Frontiers in Microbiology
The phylum Actinobacteria is one of the most ubiquitously present bacterial lineages on Earth. In the present study, we try to explore the diversity of cultivable rare Actinobacteria in Sigangli Cave, Yunnan, China by utilizing a combination of different sample pretreatments and under different culture conditions. Pretreating the samples under different conditions of heat, setting the isolation condition at different pHs, and supplementation of media with different calcium salts were found to be effective for isolation of diverse rare Actinobacteria. During our study, a total of 204 isolates affiliated to 30 genera of phylum Actinobacteria were cultured. Besides the dominant Streptomyces, rare Actinobacteria of the
Actinomycetes inhabiting granitic rocks at St. Katherine, Egypt were investigated for their bioweathering potential. Actinomycete counts ranged between 174 and 360 colony forming units per gram. Counts were positively correlated to rock porosity (r=0.65) and negatively correlated to rock salinity (r=−0.56). Sixty-six actinomycete isolates originating from rocks could be assigned into eight genera, with a high frequency of Nocardioides and Streptomyces. Organic acids were produced by 97% of the isolates. Strains belonging to Actinopolyspora, Actinomadura, Kitasatospora, Nocardioides, and Kibdelosporangium showed the highest acid production indices. Representatives from all eight genera could precipitate metals Cu, Fe, Zn, Cd, and Ag up to concentrations of 2.5 mM each. An actinomycete consortium of two Nocardioides strains and one Kibdelosporangium strain was studied for its potential to cause rock weathering in batch experiments. Results indicated a high ability of the consortium to leach the metals Cu, Zn, and Fe up to 2.6-, 2.1-, and 1.3-fold, respectively, compared to the control after 4 weeks. The pH significantly decreased after 1 week, which was parallel to an increased release of phosphate and sulfate reaching a 2.2-and 2.5-fold increase, respectively, compared to control. Highly significant weight loss (p= 0.005) was achieved by the consortium, indicating a potential multiple role of actinomycetes in weathering by acid production, metal leaching, and solubilization of phosphate and sulfate. This study emphasizes the diverse and unique abilities of actinomycetes inhabiting rock surfaces which could be of potential biotechnological applications, such as in the bioremediation of metalcontaminated environments and metal biorecovery.
The importance of microbiological activity in the alteration of natural basaltic glass
Geochimica et Cosmochimica Acta, 1992
The textural development of palagonite may differ profoundly depending on whether alteration occurred in the outermost 6-7 mm thick light-exposed surface zone of deposits, or elsewhere. In the former case, a pit-textured development of the parent basaltic glass develops as a consequence of local establishment of a highly alkaline micro-environment (pH > 9) for which the light-dependent cryptoendolithic cyanobacteria are considered most likely to be responsible. A highly porous, sponge-textured variety of palagonite, frequently defining zoned layers, contains abundant examples of bacteria. The shape and size of the pores combined with the geochemical development strongly suggest that bacteria have played an important role in the development of this texture.
Bacterial Diversity of Terrestrial Crystalline Volcanic Rocks, Iceland
Bacteria inhabiting crystalline rocks from two terrestrial Icelandic volcanic lava flows of similar age and from the same geographical region, but differing in porosity and mineralogy, were characterised. Microarray (PhyloChip) and clone library analysis of 16S rRNA genes revealed the presence of a diverse assemblage of bacteria in each lava flow. Both methods suggested a more diverse community at the Dómadalshraun site (rhyolitic/andesitic lava flow) than that present at the Hnausahraun site (basaltic lava flow). Proteobacteria dominated the clone library at the Dómadalshraun site, while Acidobacteria was the most abundant phylum in the Hnausahraun site. Although analysis of similarities of denaturing gradient gel electrophoresis profiles suggested a strong correlation of community structure with mineralogy, rock porosity may also play an important role in shaping the bacterial community in crystalline volcanic rocks. Clone sequences were most similar to uncultured microorganisms, mainly from soil environments. Of these, Antarctic soils and temperate rhizosphere soils were prominent, as were clones retrieved from Hawaiian and Andean volcanic soils. The novel diversity of these Icelandic microbial communities was supported by the finding that up to 46% of clones displayed <85% sequence identities to sequences currently deposited in the RDP database.
Scientific Reports
The orthoquartzite Imawarì Yeuta cave hosts exceptional silica speleothems and represents a unique model system to study the geomicrobiology associated to silica amorphization processes under aphotic and stable physical–chemical conditions. In this study, three consecutive evolution steps in the formation of a peculiar blackish coralloid silica speleothem were studied using a combination of morphological, mineralogical/elemental and microbiological analyses. Microbial communities were characterized using Illumina sequencing of 16S rRNA gene and clone library analysis of carbon monoxide dehydrogenase (coxL) and hydrogenase (hypD) genes involved in atmospheric trace gases utilization. The first stage of the silica amorphization process was dominated by members of a still undescribed microbial lineage belonging to the Ktedonobacterales order, probably involved in the pioneering colonization of quartzitic environments. Actinobacteria of the Pseudonocardiaceae and Acidothermaceae familie...
Bacterial diversity of weathered terrestrial Icelandic volcanic glasses
Microbial Ecology, 2010
The diversity of microbial communities inhabiting two terrestrial volcanic glasses of contrasting mineralogy and age was characterised. Basaltic glass from a <0.8 Ma hyaloclastite deposit (Valafell) harboured a more diverse Bacteria community than the younger rhyolitic glass from ∼150-300 AD (Dόmadalshraun lava flow). Actinobacteria dominated 16S rRNA gene clone libraries from both sites, however, Proteobacteria, Acidobacteria and Cyanobacteria were also numerically abundant in each. A significant proportion (15-34%) of the sequenced clones displayed <85% sequence similarities with current database sequences, thus suggesting the presence of novel microbial diversity in each volcanic glass. The majority of clone sequences shared the greatest similarity to uncultured organisms, mainly from soil environments, among these clones from Antarctic environments and Hawaiian and Andean volcanic deposits. Additionally, a large number of clones within the Cyanobacteria and Proteobacteria were more similar to sequences from other lithic environments, included among these Icelandic clones from crystalline basalt and rhyolite, however, no similarities to sequences reported from marine volcanic glasses were observed. PhyloChip analysis detected substantially greater numbers of phylotypes at both sites than the corresponding clone libraries, but nonetheless also identified the basaltic glass community as the richer, containing approximately 29% unique phylotypes compared to rhyolitic glass
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