Geomicrobiology

Call for Papers 8th International Conference on Bioscience & Engineering (BIOE 2022) will provide an excellent international forum for sharing knowledge and results, in theory, methodology and applications impacts and challenges of Bioscience and Engineering. The conference documents practical and theoretical results which make a fundamental contribution to the development of Bioscience and Engineering. The aim of the conference is to provide a platform to the researchers and practitioners from both academia as well as industry to meet and share cutting-edge development in the field.

5th International Conference on Bioscience & Engineering (BIOSE 2022) will provide an excellent international forum for sharing knowledge and results in theory, methodology and applications impacts and challenges of Bioscience and Engineering. The conference documents practical and theoretical results which make a fundamental contribution for the development of Bioscience and Engineering. The aim of the conference is to provide a platform to the researchers and practitioners from both academia as well as industry to meet and share cutting-edge development in the field.

5th International Conference on Bioscience & Engineering (BIOSE 2022) will provide an
excellent international forum for sharing knowledge and results in theory, methodology and applications impacts and challenges of Bioscience and Engineering. The conference
documents practical and theoretical results which make a fundamental contribution for the development of Bioscience and Engineering. The aim of the conference is to provide a platform to the researchers and practitioners from both academia as well as industry to meet and share cutting-edge development in the field.

5th International Conference on Bioscience & Engineering (BIOSE 2022) will provide an excellent international forum for sharing knowledge and results in theory, methodology and applications impacts and challenges of Bioscience and Engineering. The conference documents practical and theoretical results which make a fundamental contribution for the development of Bioscience and Engineering. The aim of the conference is to provide a platform to the researchers and practitioners from both academia as well as industry to meet and share cutting-edge development in the field. The goal of this Conference is to bring together researchers and practitioners from academia and industry to focus on Bioscience and Engineering advancements, and establishing new collaborations in these areas. Original research papers, state-of-the-art reviews are invited for publication in all areas of Bioscience and Engineering.

Peritidal ferruginous microbialites form the main bulk of the Middle Eocene ironstone deposits of the Bahariya Depression, Western Desert, Egypt. They include ferruginous stromatolites and microbially coated grains (ferruginous oncoids and ooids). Their internal structures reveal repeated cycles of microbial and Fe oxyhydroxide laminae. The microbial laminae consist of fossilised neutrophilic filamentous iron-oxidising bacteria. These bacteria oxidised the Fe(II)-rich acidic groundwater upon meeting the marine water at an approximately neutral pH. The iron oxyhydroxide laminae were initially precipitated as amorphous iron oxhydroxides and subsequently recrystallised into nanocrystalline goethite during early diagenesis. Organic remains such as proteinaceous compounds, lipids, carbohydrates and carotenoids are preserved and can be identified by Raman spectroscopy. The ferruginous microbialites were subjected to post-depositional subaerial weathering associated with sea-level retreat and subsurface alteration by continued ascent of the Fe(II)-rich acidic groundwater. At this stage, another iron-oxidising bacterial generation prevailed in the acidic environment. The acidity of the groundwater was caused by oxidation of pyrite in the underlying Cenomanian Bahariya formation. The positive iron isotopic ratios and presence of ferrous and ferric iron sulphates may result from partial iron oxidation along the redox boundary in an oxygen-depleted environment.

The Erreketa cave (Gipuzkoa, Basque Country) is developed in a bar of marbles and black marly limestone of Turonian age (late Cretaceous) intruded by basic-ultrabasic sills of the base of the late Cretaceous volcanic complex of the Basque-Cantabrian Basin. It has an underground river of 380 m of development and -10 m of unevenness, which discharges through a lower upwelling. The cave ecosystem was studied through the use of attractive baits, filtered with plankton nets and direct collection aquatic traps. In the cavity inhabit mammals and cave invertebrates, highlighting an interesting set of stygobite crustaceans. In addition, the cavity has various geo-microbiological features of interest. The works carried out are illustrated with digital photography.

One sentence summary: This study gives insight into the bacterial community composition related to iron-cycling in suboxic marine sediments based on 16S rRNA gene pyrosequencing. ABSTRACT To gain insight into the bacterial communities involved in iron-(Fe) cycling under marine conditions, we analysed sediments with Fe-contents (0.5–1.5 wt %) from the suboxic zone at a marine site in the Skagerrak (SK) and a brackish site in the Bothnian Bay (BB) using 16S rRNA gene pyrosequencing. Several bacterial families, including Desulfobulbaceae, Desulfuromonadaceae and Pelobacteraceae and genera, including Desulfobacter and Geobacter, known to reduce Fe were detected and showed highest abundance near the Fe(III)/Fe(II) redox boundary. Additional genera with microorganisms capable of coupling fermentation to Fe-reduction, including Clostridium and Bacillus, were observed. Also, the Fe-oxidizing families Mariprofundaceae and Gallionellaceae occurred at the SK and BB sites, respectively, supporting Fe-cycling. In contrast, the sulphate (SO 4 2−) reducing bacteria Desulfococcus and Desulfobacterium were more abundant at greater depths concurring with a decrease in Fe-reducing activity. The communities revealed by pyrosequencing, thus, match the redox stratification indicated by the geochemistry, with the known Fe-reducers coinciding with the zone of Fe-reduction. Not the intensely studied model organisms, such as Geobacter spp., but rather versatile microorganisms, including sulphate reducers and possibly unknown groups appear to be important for Fe-reduction in these marine suboxic sediments.

Limestone caves often present interesting examples of geomicrobiological interactions, little known. In this work, we present data on two cavities of moderate dimensions located in an outcrop of Urgonian reef limestones in the Mala erreka valley. The cavities have tapestries of algae and bacteria of contrasting colours. The activity of the microorganisms alters the rock and the calcite speleothems, forming moonmilk and thin cottony coatings of acicular crystals of gypsum. We report the finding of a new colony of bats Rhinolophus ferrumequinum (Schreber) and additional data on cave fauna.

There is increasing evidence that Mars may have once been a habitable environment. Gypsum is targeted in the search for Martian biosignatures because it can host extensive cryptoendolithic communities in extreme terrestrial environments and is widespread on Mars. In this study the viability of using different spectroscopy-based techniques to identify the presence of gypsum endolithic communities was investigated by analysing various cryptoendoliths collected from the Lake St. Martin impact crater (LSM), a Mars analogue site found in Manitoba, Canada. Concurrently, the cryptoendolithic microbial community structure present was also analysed to aid in assigning spectroscopic features to microbial community members. Two main morphologies of endolithic communities were collected from gypsum deposits at LSM: true cryptoendolithic communities and annular deposits on partially buried boulders and cobbles <1 cm below the soil surface. Endolithic communities were found to be visibly present only in gypsum with a high degree of translucency and could occur as deep as 3 cm below the exterior surface. The bacterial community was dominated by a phylum (Chloroflexi) that has not been previously observed in gypsum endoliths. The exterior surfaces of gypsum boulders and cobbles are devoid of spectroscopic features attributable to organic molecules and detectable by reflectance, Raman, or ultraviolet-induced fluorescence spectroscopies. However, exposed interior surfaces show unique endolithic signatures detectable by each spectroscopic technique. This indicates that cryptoendolithic communities can be detected via spectroscopy-based techniques, provided they are either partially or fully exposed and enough photon–target interactions occur to enable detection.

Precipitation of calcium carbonate (CaCO3(s)) can be driven by microbial activity. Here, a systematic approach is used to identify the morphological and mineralogical characteristics of CaCO3(s) precipitated during the heterotrophic growth of micro-organisms isolated from polar environments. Focus was placed on establishing mineralogical features that are common in bioliths formed during heterotrophic activity, while in parallel identifying features that are specific to bioliths precipitated by certain microbial phylotypes. Twenty microbial isolates that precipitated macroscopic CaCO3(s) when grown on B4 media supplemented with calcium acetate or calcium citrate were identified. A multimethod approach, including scanning electron microscopy, high-resolution transmission electron microscopy, and micro-X-ray diffraction (μ-XRD), was used to characterize CaCO3(s) precipitates. Scanning and transmission electron microscopy showed that complete CaCO3(s) crystal encrustation of Arthrobacter sp. cells was common, while encrustation of Rhodococcus sp. cells did not occur. Several euhedral and anhedral mineral formations including disphenoid-like epitaxial plates, rhomboid-like aggregates with epitaxial rhombs, and spherulite aggregates were observed. While phylotype could not be linked to specific mineral formations, isolates tended to precipitate either euhedral or anhedral minerals, but not both. Three anhydrous CaCO3(s) polymorphs (calcite, aragonite, and vaterite) were identified by μ-XRD, and calcite and aragonite were also identified based on TEM lattice-fringe d value measurements. The presence of certain polymorphs was not indicative of biogenic origin, although several mineralogical features such as crystal-encrusted bacterial cells, or casts of bacterial cells embedded in mesocrystals are an indication of biogenic origin. In addition, some features such as the formation of vaterite and bacterial entombment appear to be linked to certain phylotypes. Identifying phylotypes consistent with certain mineralogical features is the first step toward discovering a link between these crystal features and the precise underlying molecular biology of the organism precipitating them.

In this study, among a collection of heavy metals resistant endophytic bacterial strains isolated from aquatic hyperaccumulator plant (Eichhornia crassipes), one plant growth promoting endophytic bacteria (PGPE), SVUB4 was selected for its ability to utilize 1-aminocyclopropane-1-carboxylic acid (ACC) as the sole N source and accumulate different heavy metals. The SVUB4 strain was characterized as Enterobacter sp. on the basis of its 16S rDNA sequences. Assessment of the parameters of plant growth promotion revealed the intrinsic ability of the strain for the production of IAA, siderophore and solubilization of insoluble phosphate. Furthermore, plasmid DNA analysis of Enterobacter sp. strain SVUB4 indicated the presence of a single large plasmid element. The results of plasmid curing experiments demonstrated that the ability of this strain to grow in presence of Cd and Zn was encoded by the 98 kb plasmid, whereas the ability to grow in the presence of Pb appeared to be encoded by the chromosome. The Cd and Zn removal capacity of the respective metal sensitive strain (plasmidless) were about 36 and 45 μg/g-1 DW, respectively, while the removal capacity of the both metal by metal resistant strain (p SVUB4) showed a significantly higher Cd and Zn removal capacity of 153 and 228 μg/g−1 DW, respectively. However, both strains exhibited a similar pattern of Pb accumulation. The present observation also showed that for wild-type strain SVUB4 (pSVUB4), the overall level of IAA production in the absence and in the presence of Cd2+ or Zn2+was approximately the same. Nevertheless, strain SVUB4M in this respect appeared to be more sensitive to heavy metals: a noticeable decrease in IAA production was observed under the effect of both metals, especially with Cd2+.

5 th International Conference on Bioscience & Engineering (BIOSE 2022) will provide an excellent international forum for sharing knowledge and results in theory, methodology and applications impacts and challenges of Bioscience and Engineering. The conference documents practical and theoretical results which make a fundamental contribution for the
development of Bioscience and Engineering. The aim of the conference is to provide a platform to the researchers and practitioners from both academia as well as industry to meet and share cutting-edge development in the field.

Hyperalkaline surface environments can occur naturally or because of contamination by hydroxide-rich wastes. The high pH produced in these areas has the potential to lead to highly specialised microbial communities and unusual biogeochemical processes. This paper reports an investigation into the geochemical processes that are occurring in a buried, saturated, organic–rich soil layer at pH 12.3. The soil has been trapped beneath calcite precipitate (tufa) that is accumulating where highly alkaline leachate from a lime kiln waste tip is emerging to atmosphere. A population of anaerobic alkaliphilic bacteria dominated a single, unidentified specie within the Comamonadaceae family of β-proteobacteria has established itself near the top of the soil layer. This bacterial population appears to be capable of nitrate reduction using electron donors derived from the soil organic matter. Below the zone of nitrate reduction a significant proportion of the 0.5N HCl extractable iron (a proxy for microbial available iron) is in the Fe(II) oxidation state indicating there is increasing anoxia with depth and suggesting that microbial iron reduction is occurring.

Scope 7th International Conference on Bioscience & Engineering (BIOE 2021) will provide an excellent international forum for sharing knowledge and results, in theory, methodology and applications impacts and challenges of Bioscience and Engineering. The conference documents practical and theoretical results which make a fundamental contribution to the development of Bioscience and Engineering. The aim of the conference is to provide a platform to the researchers and practitioners from both academia as well as industry to meet and share cutting-edge development in the field. The goal of this Conference is to bring together researchers and practitioners from academia and industry to focus on Bioscience and Engineering advancements and establishing new collaborations in these areas. Original research papers, state-of-the-art reviews are invited for publication in all areas of Bioscience and Engineering.

Diatoms have evolved an obligate requirement for silica for their ornamented cell wall. Diatom productivity and subsequent burial of their siliceous remains on the ocean floor is a major control on the marine silica cycle. The ecological success of the diatoms over the Mesozoic and Cenozoic is associated with biogeographic shifts in siliceous sponges, decreasing silicification in the radiolarians, and a global decrease in oceanic silicic acid concentrations. We review what is known about the evolutionary advantages of the silica frustule and how selection pressures, including decreasing silicic acid concentrations, changes in growth limiting nutrients other than Si, CO2, irradiance, predation and viral pressures have shaped the morphology of the frustule over the Mesozoic and Cenozoic.

ABSTRACTThe biochemical and molecular mechanisms used by alkaliphilic bacterial communities to reduce metals in the environment are currently unknown. We demonstrate that an alkaliphilic (pH &gt; 9) consortium dominated byTissierella,Clostridium, andAlkaliphilusspp. is capable of using iron (Fe3+) as a final electron acceptor under anaerobic conditions. Iron reduction is associated with the production of a freely diffusible species that, upon rudimentary purification and subsequent spectroscopic, high-performance liquid chromatography, and electrochemical analysis, has been identified as a flavin species displaying properties indistinguishable from those of riboflavin. Due to the link between iron reduction and the onset of flavin production, it is likely that riboflavin has an import role in extracellular metal reduction by this alkaliphilic community.

Serpentinization-fueled systems in the cool, hydrated forearc mantle of subduction zones may provide an environment that supports deep chemolithoautotrophic life. Here, we examine ser-pentinite clasts expelled from mud volcanoes above the Izu–Bonin– Mariana subduction zone forearc (Pacific Ocean) that contain complex organic matter and nanosized Ni–Fe alloys. Using time-of-flight secondary ion mass spectrometry and Raman spectroscopy, we determined that the organic matter consists of a mixture of aliphatic and aromatic compounds and functional groups such as amides. Although an abiotic or subduction slab-derived fluid origin cannot be excluded, the similarities between the molecular signatures identified in the clasts and those of bacteria-derived biopolymers from other serpentinizing systems hint at the possibility of deep microbial life within the forearc. To test this hypothesis, we coupled the currently known temperature limit for life, 122 °C, with a heat conduction model that predicts a potential depth limit for life within the forearc at ∼10,000 m below the seafloor. This is deeper than the 122 °C isotherm in known oceanic serpentinizing regions and an order of magnitude deeper than the downhole temperature at the serpentinized Atlantis Massif oceanic core complex, Mid-Atlantic Ridge. We suggest that the organic-rich serpentinites may be indicators for microbial life deep within or below the mud volcano. Thus, the hydrated forearc mantle may represent one of Earth's largest hidden microbial ecosystems. These types of protected ecosystems may have allowed the deep biosphere to thrive, despite violent phases during Earth's history such as the late heavy bombardment and global mass extinctions. deep biosphere | serpentinization | subduction zone | forearc

Planetary protection regulations are in place to control the contamination of planets and moons with terrestrial micro-organisms in order to avoid jeopardizing future scientific investigations relating to the search for life. One environmental chemical factor of relevance in extraterrestrial environments, specifically in the moons of the outer solar system, is ammonia (NH3). Ammonia is known to be highly toxic to micro-organisms and may disrupt proton motive force, interfere with cellular redox reactions or cause an increase of cell pH. To test the survival potential of terrestrial micro-organisms exposed to such cold, ammonia-rich environments, and to judge whether current planetary protection regulations are sufficient, soil samples were exposed to concentrations of NH3 from 5 to 35% (v/v) at −80°C and room temperature for periods up to 11 months. Following exposure to 35% NH3, diverse spore-forming taxa survived, including representatives of the Firmicutes (Bacillus, Sporosarcina, Viridibacillus, Paenibacillus, Staphylococcus and Brevibacillus) and Actinobacteria (Streptomyces). Non-spore forming organisms also survived, including Proteobacteria (Pseudomonas) and Actinobacteria (Arthrobacter) that are known to have environmentally resistant resting states. Clostridium spp. were isolated from the exposed soil under anaerobic culture. High NH3 was shown to cause a reduction in viability of spores over time, but spore morphology was not visibly altered. In addition to its implications for planetary protection, these data show that a large number of bacteria, potentially including spore-forming pathogens, but also environmentally resistant non-spore-formers, can survive high ammonia concentrations.

In the north-central part of the Urbasa mountain range, to the W of the stone huts of the shepherds of Etxarri, there exists among many others a large dolina or depression with a singular feature: one of its edges is sunken and forms a large vault called Lezaundi or Lezeaundi. The huge mouth is 102 m long by 72 m wide and 35 m high. This rock shelter is situated in an area of massive absorption. In its bottom open several small mouths that lead to a net of abysses, halls and galleries of 440 m development and -70 m depth. The cavity is developed in a unit of massive calcarenites with nummulites of Lutecian age (Eocene, Tertiary marine), which overlaps an alternation of limestones and marls of Ilerdian age (basal Eocene). Several cave dwelling invertebrates inhabit the cavity, including various troglobites species. The work describes the main features of the cave and its cave ecosystem.