Involvement of Microorganisms in the Formation of Carbonate Speleothems in the Cervo Cave (L'Aquila-Italy)

Much is known about the bacterial precipitation of carbonate rocks, but comparatively little is known about the involvement of microbes in the formation of secondary mineral structures in caves. We hypothesized that bacteria isolated from calcareous stalactites, which are able to mediate CaCO₃ precipitation in vitro, play a role in the formation of carbonate speleothems. We collected numerous cultivable calcifying bacteria from calcareous speleothems from Cervo cave, implying that their presence was not occasional. The relative abundance of calcifying bacteria among total cultivable microflora was found to be related to the calcifying activity in the stalactites. We also determined the δ ¹³C and δ ¹⁸ O values of the Cervo cave speleothems from which bacteria were isolated and of the carbonates obtained in vitro to determine whether bacteria were indeed involved in the formation of secondary mineral structures. We identified three groups of biological carbonates produced in vitro at 11°C on the basis of their carbon isotopic composition: carbonates with δ ¹³C values (a) slightly more positive, (b) more negative, and (c) much more negative than those of the stalactite carbonates. The carbonates belonging to the first group, characterized by the most similar δ ¹³C values to stalactites, were produced by the most abundant strains. Most of calcifying isolates belonged to the genus Kocuria. Scanning electron microscopy showed that dominant morphologies of the bioliths were sherulithic with fibrous radiated interiors. We suggest a mechanism of carbonate crystal formation by bacteria.     

不同风化程度钾长石表面矿物分解细菌的筛选及遗传多样性

【目的】不同风化程度钾长石表面矿物分解细菌生物多样性研究将有助于了解矿物生物风化、生物成矿和土壤形成的演化规律和机理。【方法】采用纯培养法自南平钾矿区高、中、低风化度钾长石以及矿区土壤样品中分离矿物分解细菌,通过摇瓶释硅实验比较不同菌株分解矿物能力,采用16SrDNA限制性酶切多态性分析(Amplified rDNA Restriction Analysis,ARDRA)研究了供试菌株的遗传多样性。【结果】分离筛选到35株生长良好的矿物分解细菌,与对照相比,接菌处理发酵液中有效硅增加了101～206%;所有供试菌株可分为11个OTU,分别属于5个门,6个科,7个属。多数菌株(74%)属于γ-变形杆菌纲(γ-Proteobacteria)。泛菌属(Pantoea),沙雷氏菌属(Serratia),假单胞菌属(Pseudomonas)为优势种群。【结论】南平钾矿区矿物分解细菌具有丰富的微生物种群多样性,且γ-变形杆菌纲(γ-Proteobacteria)细菌在钾长石风化过程中可能起了重要的作用。     

谈地球生物学的重要意义

地球生物学是地球科学与生命科学交叉形成的一级学科,它研究作为地球系统三大基本过程之一的生命过程,即生物圈与地球其他圈层的相互作用.不仅是地球影响生物圈.而且生物圈也影响地球系统.这种相互作用或影响,从地球历史早期到现在,是一直在协同、耦合地进行着.生命与地球环境的协同演化是地球生物学的核心.当前地球生物学发展的重点是地球微生物学.宏体生物能反映地球环境对它们的影响及它们对环境的适应,但除植物外,它们对环境的影响有限.了解生物圈与地圈双向的相互作用必须研究地球微生物学.生命科学和整个自然科学都在向微观方向发展,不断形成新的理论和技术方法.古生物学不能停留在以古动、植物学为主的阶段,而要与生命科学和整个自然科学保持同步发展.现在我们已经找到了解决微生物与地质研究相结合问题的途径.微生物功能群具有重要的地质学意义,是研究地球微生物学的突破口.地球生物学是古生物学的继承和超越.分类系统学将仍然是研究的基础,但是包含了传统古生物学的地球生物学在学科内容和技术方法上将更多地与物理、化学、生物等学科交叉融合.其结果将使古生物学在时间上更前溯,在空间上更开拓,为古生物学在地球系统科学研究和为国民经济主战场服务中开辟更广阔的前景.     

Ultra-diffuse hydrothermal venting supports Fe-oxidizing bacteria and massive umber deposition at 5000?m off Hawaii

A novel hydrothermal field has been discovered at the base of Lōihi Seamount, Hawaii, at 5000 mbsl. Geochemical analyses demonstrate that ‘FeMO Deep'', while only 0.2 °C above ambient seawater temperature, derives from a distal, ultra-diffuse hydrothermal source. FeMO Deep is expressed as regional seafloor seepage of gelatinous iron- and silica-rich deposits, pooling between and over basalt pillows, in places over a meter thick. The system is capped by mm to cm thick hydrothermally derived iron-oxyhydroxide- and manganese-oxide-layered crusts. We use molecular analyses (16S rDNA-based) of extant communities combined with fluorescent in situ hybridizations to demonstrate that FeMO Deep deposits contain living iron-oxidizing Zetaproteobacteria related to the recently isolated strain Mariprofundus ferroxydans. Bioenergetic calculations, based on in-situ electrochemical measurements and cell counts, indicate that reactions between iron and oxygen are important in supporting chemosynthesis in the mats, which we infer forms a trophic base of the mat ecosystem. We suggest that the biogenic FeMO Deep hydrothermal deposit represents a modern analog for one class of geological iron deposits known as ‘umbers'' (for example, Troodos ophilolites, Cyprus) because of striking similarities in size, setting and internal structures.     

Ediacaran microbial colonies

Enigmatic discoidal fossils are common in Neoproterozoic sedimentary sequences and in the stratigraphic record pre-date the first appearance of diverse Ediacaran fossil assemblages. Termed 'medusoids', these Neoproterozoic discoidal fossils have generally been interpreted as coelenterate-grade organisms implying a radially symmetrical body plan for ancestral eumetazoans. Analysis of exceptionally preserved discoidal fossils from the White Sea area, however, indicates that most of these discoidal forms represent colonial microbes. Localized pyritization, for example, reveals the presence of a conspicuous filamentous substructure in Ediacaria , whereas concentric rings, radial sectors and central structures in Cyclomedusa and Paliella compare directly with Recent microbial colonies growing in a nutritionally heterogeneous environment. At least some Ediacaran discoids can be compared with extant concentric ring-shaped microbial colonies that grow in hypersaline microbial mats. Insofar as most of the remaining record of Ediacaran discoids can be attributed to the holdfast structures of non-radiate modular organisms, there is no support from the fossil record for identifying a radiate ancestry for the Metazoa.     

Interaction of the sulfur and iron cycles in the Tinto River ecosystem

The identification, in the Tinto River (IberianPyritic Belt), of iron- and sulfur-oxidizingprokaryotes responsible for the extremeconditions of acidity (mean pH 2.3) and highconcentration of heavy metals found in itswaters (Fe, Cu, Zn, As, Cr), together withiron- and sulfur-reducing prokaryoticactivities, strongly suggest the coupledoperation of the iron and the sulfur cycles inthis ecosystem.     

Carbonate Mineralogy Along a Biogeochemical Gradient in Recent Lacustrine Sediments of Gallocanta Lake (Spain)

Three sedimentary subenvironments, palustrine (GP), marginal lacustrine (GML) and central lacustrine (GCL), were compared regarding water chemistry and microbial activity in order to explain the differences in the carbonate mineralogical composition of the upper sediment layer in Gallocanta Lake, a shallow hypersaline environment in Northeastern Spain. Horizontal heterogeneity was considerable, salinity ranged from 5 to 116 (‰) for the GP and GCL subenvironments respectively. Sulfate, Mg ^{2 +} , and Ca ^{2 +} concentrations covaried among them and with salinity. The relative abundance of Mg-bearing carbonates, including high-Mg calcite, dolomite and hydrated Ca-magnesite, increased with the salinity. They were absent from the GP subenvironment, where only calcite precipitates, and maximum abundances were found in the GCL subenvironment (61%), where salinity, sulfate, and Mg ²⁺ concentrations were highest. Every subenvironment presented specific microecological characteristics. The microbial community of the GCL subenvironment lacked of oxygenic photosynthesis, while the microbial communities of GML and GP subenvironments were photosynthetically active. Vertical profiles of sulfide and pH at the water-sediment interface revealed clear differences between the GCL and GML subenvironments as well. Sulfide was detected below the oxic layer in the GCL subenvironment and increased with depth, but it was undetected in the GML subenvironment. The precipitation of Mg-bearing carbonates with different Mg:Ca proportions occurs at different stage along a biogeochemical gradient, where increasing salinity and sulfate content favour the anaerobic oxidation of organic carbon by dissimilatory sulfate reduction.     

Mineralogical Footprints of Bacterial Biofilms Associated with Labit Cave,a Part of the Longest Cave System in India

The present study was an attempt to demonstrate the capabilities of the microbial strains from the unexplored Labit cave in India to precipitate calcite providing evidence for biotic processes involved in formation of speleothem deposits. Six calcifying bacterial strains majority belonging to genus Bacillus were isolated from the cave. SEM studies revealed an array of various in vitro crystal polymorphs generated by the isolated bacteria which are similar to microscopic observations on natural formations in speleothems. The EDX spectrum of the precipitated crystals predominately composed of calcium carbonate indicating the relevance of bacterial biofilm in cave geomicrobiology and biogenic evolution of cave formations in the studied cave, which is further supported by XRF analysis and Raman spectroscopy.     

Ecophysiology and geochemistry of microbial arsenic oxidation within a high arsenic, circumneutral hot spring system of the Alvord Desert

Microbial metabolism of arsenic has gained considerable interest, due to the potential of microorganisms to drive arsenic cycling and significantly influence the geochemistry of naturally arsenic-rich or anthropogenically arsenic-polluted environments. Alvord Hot Spring in southeastern Oregon is a circumneutral hot spring with an average arsenic concentration of 4.5 mg L(-1) (60 microM). Hydrogeochemical analyses indicated significant arsenite oxidation, increased pH and decreased temperature along the stream channels flowing into Alvord Hot Spring. The dynamic range of pH and temperature over the length of three stream channels were 6.76-7.06 and 69.5-78.2 degrees C, respectively. Biofilm samples showed As(III) oxidation ex situ. 16S rRNA gene studies of sparse upstream biofilm indicated a dominance of bacteria related to Sulfurihydrogenibium, Thermus, and Thermocrinis. The lush downstream biofilm community included these same three groups but was more diverse with sequences related to uncultured OP10 bacterial phylum, uncultured Bacteroidetes, and an uncultured clade. Isolation of an arsenite oxidizer was conducted with artificial hot spring medium and yielded the isolate A03C, which is closely related to Thermus aquaticus based on 16S rRNA gene analysis. Thus, this study demonstrated the bacterial diversity along geochemical gradients of temperature, pH and As(III): As(V), and provided evidence of microbial arsenite oxidation within the Alvord Hot Spring system.     

The Up-regulation of Carbonic Anhydrase Genes of Bacillus mucilaginosus under Soluble Ca2+ Deficiency and the Heterologously Expressed Enzyme Promotes Calcite Dissolution

Molecular mechanisms and gene regulation are of interest in the area of geomicrobiology in which the interaction between microbes and minerals is studied. This paper focuses on the regulation of the expression of carbonic anhydrase (CA) genes in Bacillus mucilaginosus and the effects of the expression product of the B. mucilaginosus CA gene in Escherichia coli on calcite weathering. Real-time fluorescent quantitative PCR (RT-qPCR) was used to explore the relationship between CA gene expression in B. mucilaginosus and promotion of calcite dissolution under condition of Ca²⁺ deficiency. The results showed that adding calcite to the medium, which lacks Ca²⁺, can up-regulate the expression of the bacterial CA genes to accelerate calcite dissolution for bacterial growth. CA genes from B. mucilaginosus were transferred into E. coli by cloning. We then employed crude enzyme extract from the resultant E. coli strain in calcite dissolution experiments. The enzyme extract promoted calcite dissolution. These findings provide direct evidence for the role of microbial CA on mineral weathering and mineral nutrition release.