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Microorganisms in the subsurface
... The concept of underground storage of radioactive wastes is applied since decades with the primary objective to permanently isolate the wastes from the biosphere (Bachofen et al., 1998;Christofi and Philip, 1997;Stroes-Gascoyne and West, 1996). As a result of these anthropogenic activities the contamination of the subterranean sediments and ground waters with uranium and other hazardous metals is a serious environmental problem worldwide. ...
... The above described microbe-metal interactions may strongly influence the fate of the hazardous metals in and outside the habitat where they have been deposited (Banaszak et al., 1999;Francis, 1998;Lloyd and Lovley, 2001;Pedersen, 1996;Selenska-Pobell, 2002). A detailed understanding of the underlying mechanisms is therefore needed to predict the future migration of the radionuclides and to develop bioremediation strategies (Bachofen et al., 1998;Pedersen, 1996). For this reason, information is required about the structure, composition, distribution and activities of the microbial communities in these extreme habitats. ...
... Deep-subsurface environments have been used for disposal of radioactive and other wastes since decades (Bachofen et al., 1998;Cho and Kim, 2000;Fredrickson et al., 2004;Nazina et al., 2004) with the primary objective to permanently isolate the injected wastes from the biosphere. The presence of viable and active microbial populations within the deep biosphere strongly influences the geochemical processes there (Ehrlich, 1998;Pedersen, 1997;Murakami et al., 2002;Jain et al., 1997). ...
Im Grundwasser des radioaktiven Endlagers Tomsk-7, Sibirien, Russland wurde die mikrobielle Diversität mittels der 16Sr DNA-Analyse untersucht. Die Ergebnisse zeigen die Dominanz von Betaproteobakterien, Bacteroidetes und einer neuen "Cyanobacteria-ähnlichen" Gruppe. Methanogene und verschiedene Cluster von Crenarcheota bestimmen die Archaeenpopulation. Autotrophe Bakterien wurden mit der RubisCO-Methode identifiziert und damit die Dominanz der Betaproteobakterien bestätigt. Aus den Gruppen der Alphaproteo- und Aktinobakterien wurden oligotrophe Bakterien isoliert. Diese tolerieren relativ hohe Konzentrationen unterschiedlicher Schwermetalle und wechselwirken effektiv mit Uran. EXAFS-Analysen haben gezeigt, dass bei pH 4,5 die Stämme U(VI) in Form von meta-Autunite immobilisieren. Bei pH 2 wurde das Uran an organische Phosphatreste gebunden. In der Umgebung des Endlagers Tomsk-7 wurden damit Mikroorganismen gefunden, die ein hohes Potential zur Bindung und zum Transport von Radionukliden haben.
... Subsurface microbiology has its roots in different disciplines, combining microbiology, geology and hydrology. Recently deep subsurface microbiology was stimulated by the search for a safe deposition of radioactive waste (Bachofen, 1998). The present research in subsurface microbiology focuses more on general microbial ecology and biogeochemistry of continental and deep sea sediments, arctic permafrost and groundwater aquifers. ...
... Department of Energy, 1983;U.S. Department of Energy, 1986;Chapelle et al., 1987;Colwell, 1989;Bachofen, 1996;Krumholz et al., 1997;Bachofen et al., 1998;Stroes-Gascoyne & Sargent, 1998). ...
... La littérature recense une altération des oxydes et métaux par l'activité bactérienne (Geesey & Flemming, 1991 ;Crolet, 1995 ;Bachofen et al., 1998 ;Beech & Gaylarde, 1999 ;Lee & Newman, 2003). En conditions anoxiques, la croissance des microorganismes peut entraîner une acidification du milieu par la production d'H 2 S ou d'acides organiques accélérant ainsi la corrosion des matériaux (Videla, 1996 ;Castaneda & Benetton, 2008). ...
... L'activité des microorganismes du biofilm est connue pour favoriser la corrosion du métal (Videla & Herrera, 2005) mais aussi la dissolution des smectites de l'encaissant (transformation des smectites de l'argile de Tournemire en gel réticulé) (Esnault, 2010 (Figure 14) (Bachofen et al., 1998). Outre l'avantage qu'ont les microorganismes à vivre au sein d'un biofilm, le rôle de ce dernier est encore très discuté vis-à-vis de la biocorrosion. ...
En France, il est envisagé de stocker en formation géologique profonde les déchets radioactifs vitrifiés à haute activité et vie longue dans un conteneur en acier inoxydable chemisé par un surconteneur en acier non allié. Les principaux produits de corrosion attendus à la surface de ce dernier, i.e. la sidérite (FeIICO3) et la magnétite (FeIIFeIII2O4), jouent un rôle protecteur contre la corrosion en tant que couche passivante. Ce travail de thèse visait à étudier l’influence des groupes métaboliques bactériens réducteurs du fer ferrique (IRB) et des nitrates (NRB) sur les transformations de ces produits de corrosion en anoxie. Des souches modèles de NRB (Klebsiella mobilis) et IRB (Shewanella putrefaciens) ont, dans un premier temps, été incubées en présence de suspension de sidérite ou de magnétite, afin d’exacerber les processus de transformation du fer du fait d’une surface spécifique élevée, puis dans un second temps, en présence de films électrogénérés de ces produits pour se rapprocher des conditions d’un acier non allié corrodé en anoxie. Ces souches bactériennes sont capables de transformer la sidérite et la magnétite par des processus microbiens directs ou indirects et de conduire à la formation de rouille verte carbonatée (FeII4FeIII2(OH)12CO3). Ce composé occupe une place centrale dans le cycle biogéochimique du fer en anoxie en tant que transitoire commun à plusieurs réactions microbiennes mobilisant le fer sous deux états d’oxydation différents FeII et FeIII. L’originalité de ce travail de thèse est donc de montrer que des métabolismes bactériens inaccoutumés tels que les NRB ou les IRB sont susceptibles de jouer un rôle dans les processus de biocorrosion
... La littérature recense une altération des oxydes et métaux par l'activité bactérienne (Geesey & Flemming, 1991 ;Crolet, 1995 ;Bachofen et al., 1998 ;Beech & Gaylarde, 1999 ;Lee & Newman, 2003). En conditions anoxiques, la croissance des microorganismes peut entraîner une acidification du milieu par la production d'H 2 S ou d'acides organiques accélérant ainsi la corrosion des matériaux (Videla, 1996 ;Castaneda & Benetton, 2008). ...
... L'activité des microorganismes du biofilm est connue pour favoriser la corrosion du métal (Videla & Herrera, 2005) mais aussi la dissolution des smectites de l'encaissant (transformation des smectites de l'argile de Tournemire en gel réticulé) (Esnault, 2010 (Figure 14) (Bachofen et al., 1998). Outre l'avantage qu'ont les microorganismes à vivre au sein d'un biofilm, le rôle de ce dernier est encore très discuté vis-à-vis de la biocorrosion. ...
Radioactive waste is one of the major problems facing the nuclear industry. To circumvent this issue France plans to store vitrified high-level nuclear waste in a stainless steel container, placed into a non-alloy steel overpack, at a depth of 500m in an argillaceous formation. The main iron corrosion products formed at the surface of the non-alloy steel are siderite (FeIICO3) and magnetite (FeIIFeIII2O4). These compounds are formed in the anoxic conditions present in the nuclear waste repository and play a protective role against corrosion as a passive layer. This work aims to investigate the activity of nitrate-reducing bacteria (NRB, Klebsiella mobilis) and iron-reducing bacteria (IRB, Shewanella putrefaciens) during the transformation of siderite and magnetite, especially those involved in anoxic iron biogeochemical cycle. Klebsiella mobilis and Shewanella putrefaciens were first incubated with siderite or magnetite suspensions (high surface specific area) in order to exacerbate the microbial iron transformation, subsequently incubated with a magnetite/siderite film synthesized by anodic polarization at applied current density. The transformation of siderite and magnetite by direct or indirect microbial processes led to the formation of carbonated green rust (FeII4FeIII2(OH)12CO3). As a transient phase shared by several bacterial reactions involving FeII and FeIII, this compound is the cornerstone of the anoxic iron biogeochemical cycle. The novelty of this thesis is the consideration of bacterial metabolisms of NRB and IRB often overlooked in biocorrosion processes.
... Water usually contains H 2 , CH 4 and CO 2 that are believed to promote primarily chemolithoautotrophic life. Gas concentrations are low and microbial growth is active but at low rates only [7] . ...
... A wide range of temperatures is measured depending on the geographical location and drilling depth of boreholes, therefore boreholes drilled with the purpose of exploring microbial life are rarely deeper than 1000 m and in situ temperatures are lower than 110°C [7] . ...
... Radioactive waste has been stored underground for decades with the primary objective of permanently isolating the disposed waste from the biosphere (Stroes-Gascoyne & West, 1996;Christofi & Philip, 1997;Bachofen et al., 1998). A number of countries are involved in research programs that examine the option of permanent storage of radioactive waste for the future (Pedersen, 1996;Bachofen et al., 1998). ...
... Radioactive waste has been stored underground for decades with the primary objective of permanently isolating the disposed waste from the biosphere (Stroes-Gascoyne & West, 1996;Christofi & Philip, 1997;Bachofen et al., 1998). A number of countries are involved in research programs that examine the option of permanent storage of radioactive waste for the future (Pedersen, 1996;Bachofen et al., 1998). The main concern about this method of disposal is the possibility of radioactive waste escaping and migrating into sediments and ground water. ...
Three oligotrophic bacterial strains were cultured from the ground water of the deep-well monitoring site S15 of the Siberian radioactive waste depository Tomsk-7, Russia. They were affiliated with Actinobacteria from the genus Microbacterium. The almost fully sequenced 16S rRNA genes of two of the isolates, S15-M2 and S15-M5, were identical to those of cultured representatives of the species Microbacterium oxydans. The third isolate, S15-M4, shared 99.8% of 16S rRNA gene identity with them. The latter isolate possessed a distinct cell morphology as well as carbon source utilization pattern from the M. oxydans strains S15-M2 and S15-M5. The three isolates tolerated equal amounts of uranium, lead, copper, silver and chromium but they differed in their tolerance of cadmium and nickel. The cells of all three strains accumulated high amounts of uranium, i.e. up to 240 mg U (g dry biomass)(-1) in the case of M. oxydans S15-M2. X-ray absorption spectroscopy (XAS) analysis showed that this strain precipitated U(VI) at pH 4.5 as a meta-autunite-like phase. At pH 2, the uranium formed complexes with organically bound phosphate groups on the cell surface. The results of the XAS studies were consistent with those obtained by transmission electron microscopy (TEM) and energy dispersive X-ray analysis (EDX).
... In groundwater environments, microorganisms (Bachofen, Ferloni & Flynn, 1998) and metazoa (Botosaneanu, 1986) are widespread. Here, we subsume the prokaryotic groups Archaea and Bacteria under the term "microbiome". ...
In an alluvial aquifer in the River Fulda Valley (Germany) the influence of agricultural inputs on the subterranean physical, chemical and biological relationships was examined. A 40-year-old (1977-1981) comprehensive data set on the groundwater microbiome plus metazoa was now analysed for the first time in full (measurements for up to 4 years: hydrological, chemical, physical, prokaryote, and metazoa characteristics). Four hydrogeochemically different groundwater zones were identified across the floodplain. In addition, the prokaryote (Archaea and Bacteria) and metazoan communities differed among the four zones. The hydraulic exchange between the alluvial aquifer and the River Fulda influenced the sites closest to the river, leading to the highest prokaryote and metazoan biomasses at these locations. An organic carbon plume zone of anthropogenic origin exhibited high prokaryote abundances and production, which were higher than in the surrounding mixing zone. This mixing zone represented a transition area to the river-influenced sites as well as to the fourth zone, which was characterized by high nutrient levels from intense agriculture and which exhibited low prokaryote abundance and activity and intermediate metazoan abundance. Despite high prokaryote productivity, metazoa did not favour the organic carbon plume, due probably to low oxygen concentrations. At the sites, where metazoa occurred, their biomass corresponded mostly to about one hundredth of the prokaryote biomass. The main implication from this new analysis of an old data set is that even on a coarse taxonomical resolution, patterns emerge that show – in a geologically homogeneous area – an unprecedented complexity among different groundwater zones resulting from different external influences of natural as well as anthropogenic origin. Future studies need to ascertain an adequate temporal and spatial resolution.
... Microbial communities in the terrestrial subsurface play a critical role in the biogeochemical cycles such as weathering, reduction processes and organic matter degradation [1]. Different from surface water, the aquifer displays the characteristics of a stable environment with a low level of organic carbon [2]. ...
The hydrogeological properties of groundwater and behavior of nitrate attenuation in the nitrate-polluted alluvial aquifer, Miyakonojo Basin have been investigated in previous studies, but little knowledge is known about the spatially microbial communities especially associated with nitrate depletion. The objectives of the present study are to reveal the profile of microbial communities in the alluvial aquifer, Miyakonojo Basin, and the association with environmental variations based on cloning-library approach together with hydrogeochemical variables. The results showed that high bacterial diversity was characteristic of a large number of operational taxonomic units unique to the samples. The presence of some human-/livestock related bacteria was consistent with the distribution of high nitrate concentrations, which indicated an influence of hydrogeochemical variables on microbial composition. Methane-producing archaea and ammonia-oxidizing archaea were primarily found in the anoxic and oxic environments, respectively, reflected by the distribution of welded tuff. Additionally, heterotrophic and mixo-/autotrophic denitrifiers were ubiquitously distributed, but denitrification process only occurred under the anoxic environment. Microorganisms involved in the various metabolic processes were found to coexist in the same samples. Together, this study suggested that the description of microbial communities profile and associated putative metabolic processes could reflect the hydrogeochemical conditions of the alluvial aquifer, Miyakonojo Basin.
... Aufgrund ihrer Anpassungsfähigkeit kommen Mikroorganismen auch in Habitaten vor, in denen physikalische und chemische Extreme wie hohe Temperaturen und/oder hohe Salinitäten herrschen (Rothschild und Mancinelli 2001;Pikuta et al. 2007;Morozova et al. 2010;Rampelotto 2010). Mikroorganismen sind für viele biogeochemische Prozesse relevant und stellen einen fundamentalen Bestandteil des globalen Kohlenstoff-, Schwefel-, Stickstoff-und Energiekreislaufs im Untergrund dar (Trudinger und Swaine 1979;Fredrickson et al. 1989;Bachofen et al. 1998;Griebler und Lueders 2009). Typische Konzentrationen von organischem Kohlenstoff (DOC) im Grundwasser liegen zwischen 0,2 und 15 mg/l (Thurman 1985), wobei Acetat eine wichtige Kohlenstoff-und Energiequelle der "Tiefen Biosphäre" darstellt (Wellsbury et al. 1997). ...
Zusammenfassung
In geothermischen Anlagen können Biofilme die Mineralbildung und die Injektivität von Bohrungen sowie die Materialbeständigkeit beeinträchtigen. In drei bezüglich Temperatur und Salinität sehr unterschiedlichen Anlagen waren Organismen des Schwefelkreislaufs an Betriebsstörungen beteiligt: Die erhöhte Abundanz von Sulfat-reduzierenden Bakterien (SRB) auf der kalten Seite eines Wärmespeichers wies auf deren Beteiligung an der Korrosion und der Abnahme der Injektivität hin. In allen Anlagen führte der Zutritt von Sauerstoff bzw. der Eintrag von Nitrat zu einer temporären Zunahme Schwefel-oxidierender Bakterien (SOB) und hat vermutlich Korrosionsprozesse beschleunigt. Außerdem hatte in einem Kältespeicher die temporäre Zunahme der SOB ein Filterclogging zur Folge. Aufgrund ihrer entscheidenden Rolle bei mikrobiell induzierter Korrosion (MIC) weisen Änderungen in der Abundanz von SOB und SRB auf die Ursachen mikrobiell bedingter Störungen hin. Zur Beseitigung der Störungen wurden temporäre Erhöhungen der Temperatur, Säuerungen sowie die Zugabe von Wasserstoffperoxid (H2O2) oder Nitrat in den Anlagen getestet und aus mikrobiologischer Sicht bewertet.
... The recent discovery of subsurface chemolithotrophic microorganisms participating in a radiation-free biosphere has opened an interesting perspective in astrobiology [13][14][15][16]. There is a growing list of alternative sources of lithotrophic substrates (Fe 2+ , S 2− , S 0 , As 3+ , Mn 2+ , etc.), which widens the range of metabolic versatility of this energy conservation system. ...
The geomicrobiological characterization of the water column and sediments of Río Tinto (Huelva, Southwestern Spain) have proven the importance of the iron and the sulfur cycles, not only in generating the extreme conditions of the habitat (low pH, high concentration of toxic heavy metals), but also in maintaining the high level of microbial diversity detected in the basin. It has been proven that the extreme acidic conditions of Río Tinto basin are not the product of 5000 years of mining activity in the area, but the consequence of an active underground bioreactor that obtains its energy from the massive sulfidic minerals existing in the Iberian Pyrite Belt. Two drilling projects, MARTE (Mars Astrobiology Research and Technology Experiment) (2003–2006) and IPBSL (Iberian Pyrite Belt Subsurface Life Detection) (2011–2015), were developed and carried out to OPEN ACCESS Life 2014, 4 512 provide evidence of subsurface microbial activity and the potential resources that support these activities. The reduced substrates and the oxidants that drive the system appear to come from the rock matrix. These resources need only groundwater to launch diverse microbial metabolisms. The similarities between the vast sulfate and iron oxide deposits on Mars and the main sulfide bioleaching products found in the Tinto basin have given Río Tinto the status of a geochemical and mineralogical Mars terrestrial analogue.
... The recent discovery of subsurface chemolithotrophic microorganisms participating in a radiation-free biosphere has opened an interesting perspective in astrobiology [13][14][15][16]. There is a growing list of alternative sources of lithotrophic substrates (Fe 2+ , S 2− , S 0 , As 3+ , Mn 2+ , etc.), which widens the range of metabolic versatility of this energy conservation system. ...
The geomicrobiological characterization of the water column and sediments of Río Tinto (Huelva, Southwestern Spain) have proven the importance of the iron and the sulfur cycles, not only in generating the extreme conditions of the habitat (low pH, high concentration of toxic heavy metals), but also in maintaining the high level of microbial diversity detected in the basin. It has been proven that the extreme acidic conditions of Río Tinto basin are not the product of 5000 years of mining activity in the area, but the consequence of an active underground bioreactor that obtains its energy from the massive sulfidic minerals existing in the Iberian Pyrite Belt. Two drilling projects, MARTE (Mars Astrobiology Research and Technology Experiment) (2003-2006) and IPBSL (Iberian Pyrite Belt Subsurface Life Detection) (2011-2015), were developed and carried out to provide evidence of subsurface microbial activity and the potential resources that support these activities. The reduced substrates and the oxidants that drive the system appear to come from the rock matrix. These resources need only groundwater to launch diverse microbial metabolisms. The similarities between the vast sulfate and iron oxide deposits on Mars and the main sulfide bioleaching products found in the Tinto basin have given Río Tinto the status of a geochemical and mineralogical Mars terrestrial analogue.
... The detailed geochemical characterization (Descourvieres et al., 2010) of the aquifer has facilitated a conceptual understanding of the key geochemical processes that will take place with MAR operations and is of value to reliably predict eminent microbiological processes. The importance of having a good knowledge of concentrations and species of organic carbon, different types and concentrations of electron acceptors or other nutrients, hydraulic conductivity, texture, porosity, surface area, and mineralogy of the aquifer has been highlighted as important to develop a holistic understanding of subsurface microbial ecology (Pedersen, 1993; Bachofen et al., 1998). Subsurface microbial ecology investigations thus far have confirmed the basic principle 'microbes are everywhere , the environment selects' and concurrently described microbial diversity and distribution of many subsurface environments (Chandler et al., 1997a, b; Bennett et al., 2001; Musslewhite et al., 2003; Takeuchi et al., 2009; Li et al., 2012). ...
Managed aquifer recharge offers the opportunity to manage groundwater resources by storing water in aquifers when in surplus and thus increase the amount of groundwater available for abstraction during high demand. The Water Corporation of Western Australia (WA) is undertaking a Groundwater Replenishment Trial to evaluate the effects of recharging aerobic recycled water (secondary treated wastewater subjected to ultra filtration, reverse osmosis and ultra-violet disinfection) into the anaerobic Leederville aquifer in Perth, WA. Using culture independent methods, this study showed the presence of Actinobacteria, Alphaproteobacteria, Bacilli, Betaproteobacteria, Cytophagia, Flavobacteria, Gammaproteobacteria and Sphingobacteria, and a decrease of microbial diversity with an increase in depth of aquifer. Assessment of physicochemical and microbiological properties of groundwater before and after recharge revealed that recharging the aquifer with aerobic recycled water resulted in elevated redox potentials in the aquifer and increased bacterial numbers, but reduced microbial diversity. The increase of bacterial numbers and reduced microbial diversity in groundwater could be a reflection of an increased denitrifier and sulfur oxidising populations in the aquifer, as a result of the increased availability of nitrate, oxygen and residual organic matter. This is consistent with the geochemical data that showed pyrite oxidation and denitrification within the aquifer after recycled water recharge commenced. This article is protected by copyright. All rights reserved.
... It made the Government of Japan to declare State of Emergency, and an estimated 200,000 people were evacuated from the area [41]. It was for this reason that a number of countries took initiative for the research programs that examined the option of permanent storage of radioactive waste in geological formations for the future [42, 43]. But the possibility of radioactive waste escaping and migrating into sediments and groundwater was the major concern of the project. ...
Domiasiat (25�30 0 N 91�30 0 E) located in the west Khasi hill district of Meghalaya in northeast India is
one of the largest sandstone-type uranium (U) ore deposit in India containing 9.22 million tonnes of ore reserves with an average ore grade of around 0.1 % U 3 O 8 . This geographically distinct U deposit of Domiasiat is un-mined and harbours diverse group of bacteria surviving the stressful environmental conditions prevalent in the ore deposit. Studies show that the diverse bacteria belonged to 10 different bacterial groups with occurrence of some previously uncharacterized bacteria. The cultured identified
bacteria have been reported to tolerate substantial concentration of U and other metals and showed potent
capacity for uptake and precipitation of U. Studying the bacterial community associated with such pre-mined U ore deposit are advantageous as it not only generates the baseline information on microbial community structure as resourceful indicator to estimate the impact of mining to be undertaken in future but also identifies the bacteria which can be explored for their potential as bioremediation agents for radionuclide/multi-metal waste sites.
... No competing species or poisons were present that might necessitate a protective barrier of EPS. EPS could help to sorb exogenous nutrients that are unevenly distributed and irregularly supplied in many unsaturated systems such as soil (Bachofen et al., 1998). However, the EPS itself may also become a source of nutrients during starvation, as has been proposed in the unified model suggested by Laspidou & Rittman (2002). ...
Bacteria in nature grow mostly as biofilms, surface-associated cells enveloped by hydrated extracellular polymeric substances (EPS) of bacterial origin. The composite of EPS and biofilm cells is measured when quantifying bacterial biomass from natural samples. However, little is known regarding the relative magnitude of the EPS and cellular fractions of biofilm biomass, particularly in unsaturated systems such as soil and food surfaces. In this study, we examined the cellular and extracellular fractions of Pseudomonas
aeruginosa biofilms for DNA, protein and carbohydrate content. Biofilms were cultured in a model laboratory system that simulates the nutrient gradients and poorly mixed nature of unsaturated systems. We found that unsaturated biofilms exhibited two growth phases – an initial rapid phase and a second phase of slower or negligible development. However, no lag phase was observed for either carbon source. Cellular DNA accumulated linearly with biomass whereas cellular protein and carbohydrates accumulated exponentially with biomass. High levels of carbohydrate, protein and DNA were observed in the EPS of all samples, representing as much as 50% of these macromolecules in the biofilm. Most EPS accumulated during the second phase of growth, when cellular DNA increased only slightly. However, for biofilms cultured on a poorly bioavailable carbon source, EPS DNA decreased during the second phase, suggesting that EPS may affect bacterial survival under nutrient-limited conditions. Whether a product of overflow metabolism or cell lysis, EPS is a significant component of unsaturated biofilm biomass that probably impacts on bacterial ecology.
... With in situ bioremediation, both soluble and sorbed uranium(VI) can be reduced and immobilised by bacteria. In natural aquifers, mixed cultures of nitrate-, metal-and sulfate-reducing bacteria are likely to be present (Hodgkinson, 1987; Ghiorse, 1997; Nealson and Stahl, 1997; Bachofen et al., 1998). However, to date, in situ biological remediation of uranium has not been clearly demonstrated as a success in the field. ...
From the beginning of the 20th century, radioactive materials have accumulated on the earth's surface as a result of (1) the mining and processing of uranium (U) and thorium (Th) for the use and testing of nuclear weapons and for normal operations, (2) accidents in the civil nuclear power industry and, most recently, (3) the use of depleted uranium in conventional military weapons. As one of the most toxic radionuclides, uranium can disperse on soil surface by runoff, into the air by wind and to groundwater by leaching, subsequently endangering both human and animal health. Proper management of uranium-contaminated environments has therefore become an urgent need specifically in times of Nuclear Renaissance, which calls upon a holistic strategic approach from the exploitation of such natural resources, its processing in the nuclear fuel cycle to decommissioning with the appropriate considerations of environmental and radiation impacts.
... In natural aquifers mixed cultures of nitrate-, metal-and sulfate-reducing Ž bacteria are likely to be present Hodgkinson, 1987;Ghiorse, 1997;Nealson and Stahl, 1997; . Bachofen et al., 1998 . In the presence of carbon, nitrogen and phosphorus sources and adequate respective electron acceptors, these bacteria will be stimulated in the following order: denitrifying bacteria, metal-reducing bacteria, and finally sul-Ž fate-reducing bacteria Nealson and Stahl, 1997; . ...
Biological reduction of uranium is one of the techniques currently studied for in situ remediation of groundwater and subsurface soil. We investigated U(VI) reduction in groundwaters and soils of different origin to verify the presence of bacteria capable of U(VI) reduction. The groundwaters originated from mill tailings sites with U concentrations as high as 50 mg/l, and from other sites where uranium is not a contaminant, but was added in the laboratory to reach concentrations up to 11 mg/l. All waters contained nitrate and sulfate. After oxygen and nitrate reduction, U(VI) was reduced by sulfate-reducing bacteria, whose growth was stimulated by ethanol and trimetaphosphate. Uranium precipitated as hydrated uraninite (UO2·xH2O). In the course of reduction of U(VI), Mn(IV) and Fe(III) from the soil were reduced as well. During uraninite precipitation a comparatively large mass of iron sulfides formed and served as a redox buffer. If the excess of iron sulfide is large enough, uraninite will not be oxidized by oxygenated groundwater. We show that bacteria capable of reducing U(VI) to U(IV) are ubiquitous in nature. The uranium reducers are primarily sulfate reducers and are stimulated by adding nutrients to the groundwater.
... Microorganisms are widespread in the Earth's subsurface [1]. It has been estimated that the microbial biomass of the Earth's subsurface equals that in the surface biosphere [2]. ...
Microbial populations in 16 groundwater samples from six Fennoscandian Shield sites in Finland and Sweden were investigated. The average total cell number was 3.7x10(5) cells ml(-1), and there was no change in the mean of the total cell numbers to a depth of 1390 m. Culture media were designed based on the chemical composition of each groundwater sample and used successfully to culture anaerobic microorganisms from all samples between 65 and 1350 m depth. Between 0.0084 and 14.8% of total cells were cultured from groundwater samples. Sulfate-reducing bacteria, iron-reducing bacteria and heterotrophic acetogenic bacteria were cultured from groundwater sampled at 65-686 m depth in geographically distant sites. Different microbial populations were cultured from deeper, older and more saline groundwater from 863 to 1350 m depth. Principal component analysis of groundwater chemistry data showed that sulfate- and iron-reducing bacteria were not detected in the most saline groundwater. Iron-reducing bacteria and acetogens were cultured from deep groundwater that contained 0.35-3.5 mM sulfate, while methanogens and acetogens were cultured from deep sulfate-depleted groundwater. In one borehole from which autotrophic methanogens were cultured, dissolved inorganic carbon was enriched in (13)C compared to other Fennoscandian Shield groundwater samples, suggesting that autotrophs were active. It can be concluded that a diverse microbial community is present from the surface to over 1300 m depth in the Fennoscandian Shield.
... and carbon from CO 2 ) and chemosynthetically-based ecosystems are no longer considered unique (e.g., Stevens & McKinley, 1995;Stevens, 1997;Bachofen et al., 1998;Kinkle & Kane, 2000;Pedersen, 2001;Chapelle et al., 2002;Barton et al., 2007). Yet, how these microbial communities function in situ is still poorly understood and few detailed ecosystem analyses have been attempted. ...
Although ecosystems thriving in the absence of photosynthetic processes are no longer considered unique phenomena, we haveyet to understand how these ecosystems are energetically sustained via chemosynthesis. Ecosystem energetics were measuredin microbial mats from active sulfidic caves (Movile Cave, Romania; Frasassi Caves, Italy; Lower Kane Cave, Wyoming, USA; andCesspool Cave, Virginia, USA) using radiotracer techniques. We also estimated bacterial diversity using 16S rRNA sequences torelate the productivity measurements to the composition of the microbial communities. All of the microbial communities investigatedwere dominated by chemolithoautotrophic productivity, with the highest rates from Movile Cave at 281 g C/m2/yr. Heterotrophicproductivities were at least one order of magnitude less than autotrophy from all of the caves. We generated 414 new 16S rRNAgene sequences that represented 173 operational taxonomic units (OTUs) with 99% sequence similarity. Although 13% of theseOTUs were found in more than one cave, the compositions of each community were significantly different from each other (P≤0.001).Autotrophic productivity was positively correlated with overall species richness and with the number of bacterial OTUs affiliated withthe Epsilonproteobacteria, a group known for sulfur cycling and chemolithoautotrophy. Higher rates of autotrophy were also stronglypositively correlated to available metabolic energy sources, and specifically to dissolved sulfide concentrations. The relationship ofautotrophic productivity and heterotrophic cycling rates to bacterial species richness can significantly impact the diversity of highertrophic levels in chemolithoautotrophically-based cave ecosystems, with the systems possessing the highest productivity supportingabundant and diverse macro-invertebrate communities.
... The borehole windows into superdeep environments are still very few and none have been drilled with microbiology as its major motive. Boreholes drilled with the purpose of exploring microbial life are rarely deeper than 1000 m [10,11]. However, depth is not the only limiting factor for survival of deep life. ...
Intraterrestrial life has been found at depths of several thousand metres in deep sub-sea floor sediments and in the basement crust beneath the sediments. It has also been found at up to 2800-m depth in continental sedimentary rocks, 5300-m depth in igneous rock aquifers and in fluid inclusions in ancient salt deposits from salt mines. The biomass of these intraterrestrial organisms may be equal to the total weight of all marine and terrestrial plants. The intraterrestrial microbes generally seem to be active at very low but significant rates and several investigations indicate chemolithoautotrophs to form a chemosynthetic base. Hydrogen, methane and carbon dioxide gases are continuously generated in the interior of our planet and probably constitute sustainable sources of carbon and energy for deep intraterrestrial biosphere ecosystems. Several prospective research areas are foreseen to focus on the importance of microbial communities for metabolic processes such as anaerobic utilisation of hydrocarbons and anaerobic methane oxidation.
Among extremophiles, acidophiles are of special interest because their chemolithotrophic metabolism obtains energy from reduced minerals, thus creating the extreme acidic conditions in which they thrive. Rio Tinto is a 92 km long extreme acidic environment, which is the product of the metabolic activity of chemolithotrophic microorganisms thriving in the high concentration of metal sulfidic minerals existing in the Iberian Pyrite Belt. An extensive geomicrobiological characterization of the Tinto basin has proven the prominent role of the iron cycle in the ecosystem. The identification of iron sulfates and oxides on Mars, analogous to those generated in the Tinto basin by microbial metabolism, has made Rio Tinto one of the best geochemical and mineralogical terrestrial Mars analogues.
Introduction: Whilst chemolithoautotrophic micro-organisms are found in nearly every environment on Earth, they are more abundant in dark habitats where competition by photosynthetic organisms is eliminated. Caves, particularly, represent dark but accessible subsurface habitats where the importance of microbial chemolithoautotrophy to biogeochemical and geological processes can be examined directly. At Lower Kane Cave, WY, USA, hydrogen sulfide-rich springs provide a rich energy source for chemolithoautotrophic micro-organisms, supporting a surprisingly complex consortium of micro-organisms, dominated by sulfur-oxidizing bacteria. Several evolutionary lineages within the class ‘Epsilonproteobacteria’ dominate the biovolume of subaqueous microbial mats, and these microbes support the cave ecosystem through chemolithoautotrophic carbon fixation. The anaerobic interior of the cave microbial mats is a habitat for anaerobic metabolic guilds, dominated by sulfate-reducing and -fermenting bacteria. Biological controls of speleogenesis had not been considered previously and it was found that cycling of carbon and sulfur through the different microbial groups directly affects sulfuric acid speleogenesis and accelerates limestone dissolution. This new recognition of the contribution of microbial processes to geological processes provides a better understanding of the causal factors for porosity development in sulfidic groundwater systems. Karst landscapes form where soluble carbonate rocks dissolve by chemical solution (karstification), resulting in numerous geomorphic features, including caves and subterranean-conduit drainage systems (e.g. White, 1988; Ford & Williams, 1989). This has traditionally been viewed as an abiotic, chemical process that occurs near the water table, with biologically produced CO2 as the principal reactive component.
The study investigated the performance of chitosan and extracted pandan leaves towards treatment of textile wastewater by using flocculation process. Pandan leaves were extracted by using solvent extraction method. Flocculation process was conducted using a Jar test experiment. The effect of dosage, pH, and settling time on reduction of COD, turbidity and color of textile wastewater was studied. The results obtained found that chitosan was very effective for reduction of COD, turbidity, color and indicator for color. The best condition for COD and turbidity removal was achieved at 0.2 g dosage, pH 4 and 60 minutes of settling time. Under this condition, about 58 and 99% of COD and turbidity was removed, respectively. However, the results obtained using extracted pandan was opposite compared to the chitosan. Extracted pandan was not able to remove both COD and turbidity of the waste.
Introduction: Exploration of the microbial world started slowly about 350 years ago, when van Leeuwenhoek and his contemporaries first focused their microscopes on extremely small living things. It is only during the last 20 years, however, that exploration of the world of intraterrestrial microbes has gathered momentum. Previously, it had generally been assumed that persistent life could not exist deep underground, out of reach of the sun and a photosynthetic ecosystem base. In the mid-1980s, scientists started to drill deep holes, from hundreds to a thousand metres deep, in both hard and sedimentary bedrock, and up came microbes in numbers equivalent to those found in many surface ecosystems. The world of intraterrestrial microbes had been discovered. Intraterrestrial ecosystems have been reviewed elsewhere and the content of those reports need not be repeated here (Ghiorse & Wilson, 1988; Pedersen, 1993a, 2000; Bachofen, 1997; Bachofen et al., 1998; Fredrickson & Fletcher, 2001; Amend & Teske, 2005). Instead, this chapter will focus on characteristics that distinguish the intraterrestrial from the terrestrial world. Most ecosystem environments have specific, distinguishing characteristics. The environments of intraterrestrial microbial ecosystems occupy a special position, differing substantially in many respects from those of most surface-based ecosystems. In many ways, underground ecosystems must be approached quite differently from the way in which those on the surface would be approached.
Surface soils and their microbiology have been studied for decades. However, subsurface soil, more broadly referred to as the vadose zone, is of increasing interest to microbiologists. The vadose zone, extending from the terrestrial surface to the groundwater table, is rich in microbes of many types. This review summarizes what is known about the abundance and diversity of microbes in the vadose zone and the environmental factors that influence vadose zone microbes and microbial processes. We discuss the roles of vadose zone microbes in nutrient cycling as well as their importance in pollutant remediation. We address a number of fundamental questions in vadose zone microbial ecology, including: What do we need to learn about vadose zone microbes to improve our ability to predict the fates of pollutants? How different are microbial communities and microbial activities in the terrestrial subsurface compared with surface soil? Numerous questions and arguments justify " deepening " soil microbiology's spatial context to include the whole unsaturated subsurface.
We used specially designed microcosms filled with natural substrate to study microbial colonization in a shallow aquifer. Sterilized sediments were exposed to 3 types of groundwater varying in physical, chemical and biological characteristics: (1) pristine groundwater (site PI 92); (2) groundwater in an observation well at a pristine site (OMV 11); and (3) contaminated groundwater at a landfill site (OMV 5). The number of suspended bacteria was always highest at the landfill site (4.0 +/- 4,2 [standard deviation, SD] x 10(6) cells cm(-3)), i.e. on average 16 times higher than in the well water (2.5 +/- 3.0 x 10(5) cells cm(-3)) and 96 times higher than in the pristine groundwater (4.1 +/- 1.3 x 10(4) cells cm(-3)). Sediments in the microcosms were rapidly colonized and the total number of attached bacteria after 10 mo of exposure was highest at the landfill site (1.8 +/- 0.4 x 10(8) cells cm(-3)) followed by the sediment incubated in well water (1.5 +/- 0.5 x 10(8) cells cm(-3)) and in pristine groundwater (5.0 +/- 1.5 x 10(7) cells cm(-3)). As estimated from image analysis, attached cells from the landfill site were on average characterized by higher cell carbon contents (28 +/- 36 fgC cell(-1)) than at the well water (24 +/- 23 fgC cell(-1)) and the pristine groundwater site (21 +/- 23 fgC cell(-1)). The ratio of attached to suspended bacteria after 10 mo of exposure was highest in the microcosm incubated in pristine groundwater (1657:1) and lowest at the contaminated site (59:1). On the basis of our results we emphasize the importance of attached microbial communities in porous subsurface systems and underline the need for groundwater as well as sediment samples for a serious microbiological characterization of the subsurface. Furthermore, the ratio of attached to suspended bacteria in shallow aquifer systems is suggested to be an indicator of prevailing nutrient concentrations.
Transport processes in subsurface environments are determined by complex interactions between the soil matrix and dissolved as well as particulate substances. Biofilms play an important role in the transport of colloids in the subsurface, since biofilms cover the solid soil matrix and hence influence the interaction of colloids with the soil matrix. Consequently, biofilms can influence the mobility of colloids and colloid-bound contaminants either by deposition of colloids within the biofilm matrix, by remobilization of bound colloids, and/or by co-elution of colloids together with detaching biofilm compartments. Further, biofilm organisms can take part in the degradation of colloids or colloid-bound contaminants as well as in colloid generation processes.
The α-amylase of Bacillus amyloliquifaciens TSWK1-1 (GenBank Number, GQ121033) was immobilized by various methods, including ionic binding with DEAE cellulose, covalent coupling with gelatin and entrapment in polyacrylamide and agar. The immobilization of the purified enzyme was most effective with the DEAE cellulose followed by gelatin, agar and polyacrylamide. The K (m) increased, while V (max) decreased upon immobilization on various supports. The temperature and pH profiles broadened, while thermostability and pH stability enhanced after immobilization. The immobilized enzyme exhibited greater activity in various non-ionic surfactants, such as Tween-20, Tween-80 and Triton X-100 and ionic surfactant, SDS. Similarly, the enhanced stability of the immobilized α-amylase in various organic solvents was among the attractive features of the study. The reusability of the immobilized enzyme in terms of operational stability was assessed. The DEAE cellulose immobilized α-amylase retained its initial activity even after 20 consequent cycles. The DEAE cellulose immobilized enzyme hydrolyzed starch with 27 % of efficiency. In summary, the immobilization of B. amyloliquifaciens TSWK1-1 α-amylase with DEAE cellulose appeared most suitable for the improved biocatalytic properties and stability.
1. Groundwater ecosystems offer vast and complex habitats for diverse microbial communities. Here we review the current status of groundwater microbial biodiversity research with a focus on Bacteria and Archaea and on the prospects of modern techniques for enhancing our understanding of microbial biodiversity patterns and their relation to environmental conditions.
2. The enormous volume of the saturated terrestrial underground forms the largest habitat for microorganisms on earth. Up to 40% of prokaryotic biomass on earth is hidden within this terrestrial subsurface. Besides representing a globally important pool of carbon and nutrients in organisms, these communities harbour a degree of microbial diversity only marginally explored to date.
3. Although first observations of groundwater microbiota date back to Antonie van Leeuwenhoek in 1677, the systematic investigation of groundwater microbial biodiversity has gained momentum only within the last few decades. These investigations were initiated by an increasing awareness of the importance of aquifer microbiota for ecosystem services and functioning, including the provision of drinking water and the degradation of contaminants.
4. The development of sampling techniques suitable for microbiological investigations as well as the application of both cultivation-based and molecular methods has yielded substantial insights into microbial communities in contaminated aquifers, whereas knowledge of microbial biodiversity in pristine habitats is still poor at present.
5. Several novel phylogenetic lineages have been described from groundwater habitats, but to date no clearly ‘endemic’ subsurface microbial phyla have been identified. The future will show if the rather low diversity generally found in pristine oligotrophic aquifers is a fact or just a result of low abundances and insufficient resolution of today’s methods. Refined approaches complemented by statistically rigorous applications of biodiversity estimates are urgently needed.
6. Factors identified to control microbial diversity in aquifers include spatial heterogeneity, temporal variability and disturbances such as pollution with chemical anthropogenic contaminants. Although first insights into the importance of individual biogeochemical processes may be obtained from surveys of microbial diversity within functional groups, direct links to groundwater ecosystem functioning have rarely been established so far.
Molecularly imprinted polymers (MIPs) have frequently been employed as recognition elements in sensing applications, or for the controlled delivery of small molecule drugs. An equally important but less well studied application is the use of MIPs in the binding and immobilization of active enzymes. In this study, magnetic MIPs (MMIPs) recognizing the enzyme amylase were prepared using phase inversion of poly(ethylene-co-vinyl alcohol) (EVAL) solutions with 27-44 mol % ethylene in the presence of amylase. The size distribution, specific surface area, magnetization, and composition were characterized by dynamic light scattering (DLS), Brunauer-Emmett-Teller (BET) analysis, superconducting quantum interference devices (SQUID), and X-ray diffraction (XRD), respectively. The mean size of MMIPs was ~100 nm and the magnetization was 14.8 emu/g. The activities of both bound template and rebound enzyme was established by measuring glucose production via starch hydrolysis, at different temperatures, for MIPs with different compositions (wt % EVALs and mol % ethylene). The highest hydrolysis activity of MMIPs (obtained with 32 mol % ethylene) was found to be 1545.2 U/g. Finally, compared to the conventional catalysis process, MMIPs have the advantages of high surface area, suspension, easy removal from reaction, and rapid reload of enzyme. The good activity of amylase MMIPs persists after 50 cycles of starch hydrolysis.
The presence of actinides in radioactive wastes is of major concern because of their potential for migration from the waste repositories and long-term contamination of the environment. Studies have been and are being made on inorganic processes affecting the migration of radionuclides from these repositories to the environment but it is becoming increasingly evident that microbial processes are of importance as well. Bacteria interact with uranium through different mechanisms including, biosorption at the cell surface, intracellular accumulation, precipitation, and redox transformations (oxidation/reduction). The present study is intended to give a brief overview of the key processes responsible for the interaction of actinides e.g. uranium with bacterial strains isolated from different extreme environments relevant to radioactive repositories. Fundamental understanding of the interaction of these bacteria with U will be useful for developing appropriate radioactive waste treatments, remediation and long-term management strategies as well as for predicting the microbial impacts on the performance of the radioactive waste repositories.
The effects of micronutrients on growth of Thermococcus guaymasensis and Thenrmococcus aggregans in a starch-containing medium were investigated. A trace minerals solution, a vitamins solution and calcium chloride were omitted from the medium or added in different amounts. The growth rates of both species were not affected over a significant range of concentrations of these compounds, but appreciable inhibition of growth was observed after the addition of elemental sulfur to the medium. T. guaymasensis exhibited a significant tolerance to high amounts of trace element and vitamin solutions but growth was inhibited by the omission of these compounds from the medium. Moreover, both amylolytic and pullulytic activities increased in the presence of 6-fold higher amounts of trace element and vitamin solutions, compared to the concentrations used in the usual medium. In T. aggregans, both enzymatic activities were enhanced in the presence of either increased (4-fold) amounts of trace element and vitamin solutions, or after the addition of elemental sulfur to the medium. Furthermore, larger activities of starch-hydrolysing enzymes were detected with a 10-fold higher concentration of calcium chloride, compared to the usual medium, in the absence of trace element and vitamin solutions. When both Thermococcus species were tested for the tolerance to specific cations and oxyanions, T. guaymasensis exhibited higher tolerance compared to T. aggregans, the former strain being capable to grow in the presence of 6 mM Ni2+, 4mM Cu2+, 1.5 mM SeO4(2-), and 1.5 mM MoO4(2-). The content of total cell proteins followed the pattern of starch-hydrolysing enzymes and an over-expression of proteins in the range of 35, 50 and 70 kDa was observed.
A study was made on the effect of liming (Ca(OH)2) on the numbers of colony-forming units (CFU) and the biomass of fungi in loamy sand (ls) and a loose sandy soil (lss) during 90 days under laboratory conditions. Liming inhibited the growth of fungi more strongly in the lighter soil. Raising the pH of lss from its native 4.5 to 7.0 and 9.0 decreased mean fungal CFU numbers by 50%, and their biomass by 42% and 68%, respectively, in comparison with control unlimed samples. Also in ls with its native pH of 7.7, when alkalinised to 9.0 and 11.0 the fungal CFU numbers were smaller than in the control by 25% and 50%, respectively, and the fungal biomass decreased by 40% and 56%, respectively. Although in a parallel research alkalinisation has been shown to stimulate bacterial growth very strongly, especially in lss, the total microbial biomass (fungal + bacterial) declined by an average of 30% (pH 9.0) and 40% (pH 11.0) in limed ls, and by 35% (pH 7.0) and as much as 50% (pH 9.0) in lss, in comparison with the control.
Although the fact is often overlooked, proposed nuclear waste repositories in geological formations would exist in an environment quite capable of sustaining microbial life which could considerably affect containment of radionuclides. In this paper a brief review of biological tolerance of extreme environments is presented with particular reference to studies of the microbiology of deep geological formations. The possible influence of such organisms on the integrity of a waste repository and subsequent transport of radionuclides to the surface is discussed.
Responsibility for the safe disposal of radioactive waste has traditionally been the province of chemists, physicists, geologists and engineers and the potential impact of the biological sciences was not initially recognised. The deep subsurface of a high level waste (HLW) repository environment, in particular, was perceived by physical scientists as devoid of life or, even if life were present, the conditions produced by the waste would be so toxic as to render the near-field sterile. The realisation that microbial activity could influence the geological disposal of radioactive waste was first seriously discussed in the late 1970s for low/intermediate level waste (L/ILW) disposal and expanded to included deep disposal of HLW by West et al. Since this time many countries have developed programmes to determine and quantify microbial effects in terms of their own national concepts.....
Within the last few years several countries and international organisations have initiated studies of the possible influence of microbial contamination on the integrity of deep geological repositories for the disposal of high/intermediate level nuclear waste. In this paper the current status of work in this field is reviewed with particular reference the British geomicrobiology program and the practical application of resulting date in repository safety assessment.
Bacterial transport through porous media was modeled using detachment functions that incorporate the dependence of detachment rate on bacterial residence time on the collector. Model parameters and the relative merit of alternative forms for the detachment function were evaluated on the basis of comparisons between model simulations and experimentally derived bacterial breakthrough and elution curves. Only detachment functions that provided an initial period in which bacteria were rapidly released, followed by slow bacterial detachment, were able to reproduce the elution portion of the breakthrough curves. In optimal simulations, 90% of the bacteria that were captured by the porous medium detached within 1 min of attachment. Experiments involving saturated flow through columns packed with sand indicated that the time to achieve complete breakthrough was inversely related to the influent bacterial concentration. On this basis and because of the relatively slow approach to breakthrough that was typically observed in transport experiments, it was hypothesized that the experimental medium contained a number of preferred attachment sites that must be essentially filled before breakthrough is achieved. Only when such (irreversible) sorption sites were included in the model formulations was it possible to produce transport simulations that matched both the breakthrough and elution portions of the empirically derived curves. It is concluded that both a time-dependent detachment function and a degree of sorption site heterogeneity are required to describe bacterial attachment and detachment during transport as observed in our laboratory.
To investigate the distribution of microbial biomass and activities to gain insights into the physical controls on microbial activity and potential long‐term survival in the subsurface, 24 shale and sandstone cores were collected from a site in northwestern New Mexico. Bacterial biomass in the core samples ranged from below detection to 31.9 pmol total phospholipid fatty acid (PLFA) g of rock with no apparent relationship between lithology and PLFA abundance. No metabolic activities, as determined by anaerobic mineralization of [C]acetate and [C]glucose and SO4 reduction, were detected in core samples with pore throats 0.2 fan in diameter. These results suggest that subsurface bacteria require interconnected pore throats greater than 0.2 μm diameter for sustained activity but that viable bacteria can be maintained and stimulated in poorly permeable rocks, such as shales, with restrictive pore throat diameters. In addition, the detrital organic matter in the small‐pore‐diameter shales is not subject to direct microbial attack. Rather, bacteria in adjacent sandstones with a more open pore structure are probably sustained by endogenous nutrients that are slowly released from the shale. These results have implications for the long‐term maintenance of anoxia and the impact of anaerobic biogeochemical processes on groundwater chemistry.
For a long time microbial ecology has been developed as a distinct field within Ecology. In spite of the important role of microorganisms in the environment, this group of 'invisible' organisms remained unaccessable to other ecologists. Detection and identification of microorganisms remain largely dependent on isolation techniques and characterisation of pure cul tures. We now realise that only a minor fraction of the microbial com munity can be cultivated. As a result of the introduction of molecular methods, microbes can now be detected and identified at the DNA/RNA level in their natural environment. This has opened a new field in ecology: Molecular Microbial Ecology. In the present manual we aim to introduce the microbial ecologist to a selected number of current molecular techniques that are relevant in micro bial ecology. The first edition of the manual contains 33 chapters and an equal number of additional chapters will be added this year. Since the field of molecular ecology is in a continuous progress, we aim to update and extend the Manual regularly and will invite anyone to depo sit their new protocols in full detail in the next edition of this Manual. We hope this book finds its place where it was born: at the lab bench! Antoon D.L. Akkermans, Jan Dirk van Elsas and Frans J. de Bruijn March 1995 Molecular Microbial Ecology Manual 1.3.6: 1-8, 1996. © 1996 Kluwer Academic Publishers.
Transmission electron microscopy examination of bacterial cells, growing naturally in freshwater and marine environments, reveals that they can precipitate a variety of iron minerals. The development of these authigenic mineral phases may be either 'biologically controlled', whereby the cell regulates mineral formation, or 'biologically induced', with biominerals commonly generated as secondary by-products of microbe-environment interactions. With the vast majority of bacteria biomineralisation is a two-step process; initially metals are electrostatically bound to the anionic surfaces of the cell wall and surrounding organic polymers, where they subsequently serve as nucleation sites for crystal growth. Because of its relatively high activity in aqueous solutions, iron is preferentially bound to reactive organic sites. As the latter stages of mineralisation are inorganically driven,. the type of iron mineral formed is inevitably dependent on the available counter-ions, and hence, the chemical composition of the waters in which the microorganisms are growing.
Until recently, nonenzymatic processes were generally considered to account for much of the Fe(III) reduction in subsurface environments. However, it is now;clear that enzymatic Fe(III) reduction catalyzed by microorganisms which conserve energy to support growth by completely oxidizing organic compounds to carbon dioxide accounts for most of the Fe(III) reduction. Microbial Fe(III) reduction in deep pristine aquifers releases dissolved inorganic carbon into groundwater which may increase aquifer porosity. The Fe(II) released into the groundwater is an important groundwater quality problem in many aquifers. Microbial oxidation of organic contaminants coupled to Fe(III) reduction removes significant amounts of pollutants from many contaminated aquifers. Fe(III) reduction and hence contaminant removal can be accelerated in aquifer sediments with the addition of Fe(III) chelators or humic substances. Both of these amendments alleviate the need for Fe(III) reducers to come into direct physical contact with Fe(III) oxides in order to reduce them. Some Fe(III)-reducing microorganisms can reduce contaminant metals and metalloids such as uranium, technetium, cobalt, chromium and selenium. This metabolism may be useful for remediation of metal-contaminated subsurface environments. Fe(III) reducers and some of the insoluble Fe(II) products of Fe(III) reduction can reducively dechlorinate chlorinated contaminants. Magnetite that is similar to that produced by known Fe(III)-reducing microorganisms has been recovered at depths as great as 6.7 km on Earth and has been observed in a Martian meteorite. Thus, microbial oxidation of organic matter coupled to the reduction of Fe(III) to Fe(II) appears to be a important process in a variety of subsurface environments.
Recent studies have concluded that microbial contamination of a nuclear fuel waste disposal vault is inevitable. Factors that will affect the development of a substantial population of micro-organisms include physiological tolerance of microbes, fluid movement in a vault, availability of nutrients, and availability of energy sources. It is difficult to resolve whether microbial growth will either positively or negatively affect the performance of a vault. One of the necessary steps towards ultimately answering this question is to assess the potential for microbial growth in a disposal vault, based on a nutrient and energy budget. This report gives a quantitative (but conservative) inventory of nutrients and potential energy sources present in a Canadian nuclear fuel waste vault, which hypothetically could support the growth of micro-organisms.
This chapter focuses on the various methods to study the bacterial ecology of freshwater environments. This chapter discusses the bacteria in lakes that are divided into the assessment of numbers and activity with respect to synecological or autecological studies. It is not intended to provide detailed descriptions of the techniques, as virtually all the methods will have to be adapted for the habitat under study. This is particularly true of sediment systems for which reagents may have to be modified, because of the changes in the composition of the sediment. As the knowledge of the activity and interaction of aquatic bacterial populations increases the limitations of various methods become apparent. Methodology will and must continue to develop, as information or technology becomes available. Such developments will ultimately allow accurate assessment of the role of bacteria in freshwater environments.
For quantitative studies on the role of heterotrophic bacteria in the biogeochemical cycling of major elements, especially C and N, it needs to determine the values for the growth rates or productivity of the bacteria. Such values are also necessary for the analysis of food webs, involving decomposition of detritus. The methods described in the chapter are for the synecologist; they give average or composite values for all the heterotrophic bacteria. At present, the most useful method for estimating the growth rates of heterotrophic bacteria in aquatic environments is the measurement of the rates of DNA synthesis with tritiated thymidine. Adenine has also been proposed as a suitable precursor, but because it and adenosine triphosphate (ATP) are involved in many different biochemical processes and in all organisms, results are too difficult to interpret or maybe two or three orders of magnitude too high.
Mathematical modelling provides one route through which radionuclide release source terms can be determined. The DRINK 2D code is designed to provide such source terms for shallow, low level radioactive waste (LLW) repositories where significant ground water flows and a potential for microbial activity occur. A simple ID demonstration is presented here, during which the impact of an acidified and reduced environment upon the mobility and speciation of plutonium is illustrated. This environment is generated through microbial fermentation of cellulose hydrolysis products. Plutonium dissolution and re-precipitation occurs with a succession of dominant solute oxidation states starting with Pu(V), shifting to Pu(IV) and finally a mixture of Pu(III) and Pu(IV).
Publisher Summary Cell envelopes of archaea differ distinctly from those of bacteria and show remarkable structural and chemical diversity. Murein, the typical sacculus-forming polymer of bacteria, and lipopolysaccharide-containing outer membranes, characteristic of gramnegative bacteria, are not found in archaea. The pseudomurein sacculi could be isolated using the same methods as those usually applied for the isolation of the murein sacculi of gram-positive bacteria. Chemical analysis of the isolated cell wall sacculi from all species of Methanobacteriales investigated so far has revealed that none of them contains the typical murein constituents muramic acid, diaminopimelic acid, D-glutamic acid or D-alanine. Modifications of the amino-acid composition of pseudomurein could be induced by addition of glycine, threonine, ornithine, or aspartic acid in elevated concentrations to the culture medium. The synthesis of the pentapeptide moiety is supposed to start with a UDP-activated glutamic acid residue followed by the stepwise formation of UDP-activated peptides up to a pentapeptide.
The composition of microbial communities has been investigated avoiding conventional cultural techniques by chromatography-mass spectrometric analysis of chemical signature markers. Concentrations of fatty acids, hydroxy acids, aldehydes, sterols, and methanolysate of the biomass lipid fractions were used to determine the population size of the individual community members. The calculation is based on the information stored in a data bank about the chemical composition of the probable members of the community. An algorithm for rapid assessment of the genus or species composition from the total biomass GC-MS data is developed for a quantitative analysis of this community, treating them as a combination of chemical profiles of individual members. The microbial community in kaolin slurry was analyzed; it includes the following genera (in 105 cells/g): Nttrobacter (4), Bacillus (0.9), Pseudomonas (0.3), Burkholderia (0.1), Nocardia (0.4), Caulobacter (3), Deinococcus (4), Arthrobacter (0.7), Clostridium (4). Bacteroides (0.08), Desulfovibrio (1), Desulfobacter (0.3). Analyses of the profiles of unassigned components revealed the presence of two as yet unknown organisms, one being an iron-reducing bacterium designated strain FeRed, the other a microscopic fungus.
Improved understanding of the spatial and temporal distribution of microbiological properties and processes is critical due to the relative difficulty and high cost of obtaining large numbers of subsurface samples. Quantification of spatial patterns in subsurface environments is important because it is well known that geologic, hydrologic and geochemical properties are not constant in space; rather, they are spatially autocorrelated, or related over certain length scales. Preliminary research indicates that subsurface microbiological properties have similar length scales, and the microbiological properties appear to be spatially correlated to geologic, hydrologic and/or geochemical properties. Temporal variability can also be important in subsurface systems that receive seasonal recharge. In order to better understand heterogeneous subsurface systems; it is critical to sample such that the spatial and temporal patterns are adequately captured, and understand what is causing the variability and spatial patterns. Improved understanding in these two areas will yield more efficient sampling schemes, assist in defining factors that control the distribution of microbiological properties at the field scale, and increase the ability to predict and ultimately model the distribution of microbiological properties and the responses of microbial communities to environmental perturbations such as subsurface contaminant transport and bioremediation.
Metal removal by seven strains of Bacillus and Micrococcus was investigated. The culture age of the cells had little or no effect on their sorption capacity. Using the Langmuir isotherm, it was possible to determine that Bacillus subtilis ATCC 6633 had the highest maximum sorption capacity for uranium while a Micrococcus sp. strain presented the highest affinity. pH of the solution affected the sorption of uranium, copper, cadmium and zinc by B. subtilis. Hydrochloric acid was effective for desorption of uranium from pre‐loaded biomass. The presence of other ion inhibited uranium sorption in the following order: Cu2+>Zn2+>Mg2+Cd2+>Ca2+>K+.
Does there exist, deep within the earth's crust, a second biosphere--
composed of very primitive, thermophilic (heat-loving) bacteria, and
containing more living matter than the entire surface? This idea, first
proposed by the author in the early 1980s, is now supported by a growing
body of evidence. The implications are astonishing: is the deep
biosphere where life originated? Can Mars and other seemingly dead
planets contain deep biospheres? Is there yet another--deeper,
hotter--biosphere within the earth, based on silicon instead of carbon?
This is the first book to explore this very controversial, intriguing
theory.
This study investigated the distribution of bacteria in groundwater from 16 different levels in five boreholes in granite bedrock down to a maximum of 860 m. Enrichment cultures were used to assay the groups of bacteria present. Autoradiographic studies with14C- or3H-labeled formate, methanol, acetate, lactate, glucose, sodium bicarbonate, leucine, glutamine, thymidine, orN-acetyl-glucosamine were used to obtain information about bacteria active in substrate uptake. The biofilm formation potential was studied in one borehole. The chemical environment in the groundwater was anaerobic with an Eh between −112 and −383 mV, a pH usually around 8, and a temperature range of 10.2 to 20.5°C, depending on the depth. The organic content ranged between <0.5 and 9.5 mg total organic carbon liter−1. Carbon dioxide, hydrogen, hydrogen sulfide, and methane were present in the water. The nitrate, nitrite, and phosphate concentrations were close to, or below, the detection limits, while there were detectable amounts of NH
4+ in the range of 4 to 330 μg liter−1. The average total number of bacteria was 2.6×105 bacteria ml−1, as determined with an acridine organge direct-count (AODC) technique. The average number of bacteria that grew on a medium with 1.5 g liter−1 of organic substrate was 7.7×103 colony-forming units (CFU) ml−1. The majority of these were facultatively anaerobic, gram-negative, nonfermenting heterotrophs. Enrichment cultures indicated the presence of anaerobic bacteria capable of growth on C-1 compounds and hydrogen, presumably methanogenic bacteria. Most probable number assays with sulfate and lactate revealed up to 5.6×104 viable sulfate-reducing bacteria per ml. A biofilm development experiment indicated an active attached microbial population. Active substrate uptake could not be registered with the bulk water populations, except for an uptake of leucine not associated with growth. The bulk water microbial cells in deep groundwater may be inactive cells detached from active biofilms on the rock surface.
Three unsaturated subsurface paleosols influenced by moisture recharge, including a highly developed calcic paleosol, were studied to investigate the microbiology of paleosols. Two near-surface paleosols, one impacted by moisture recharge and the other beyond the influence of recharge, were also sampled to directly assess the effect of moisture recharge on the activity and composition of the microbial community associated with paleosols. The highly developed paleosol had a higher population of culturable heterotrophs, a greater glucose mineralization potential, a higher microbial diversity based on colony morphology, and a more than 20-fold higher concentration of ATP than the two weakly developed paleosols. The recharged near-surface paleosol, as compared to the near-surface paleosol unaffected by recharge, had a lower population of culturable heterotrophs, smaller mineralization rate constant, and lower richness based on colony morphology. The recharged paleosols contained predominantly gram-negative isolates, whereas the paleosol unaffected by recharge contained predominantly gram-positive isolates. Storage at 4°C of subsurface and near-surface paleosol samples containing high water potential increased the population of culturable aerobic heterotrophs, decreased diversity in colony morphology, and increased first-order rate constants and decreased lag times for glucose mineralization. These results indicate that aerobic heterotrophs are present in deep vadose zone paleosols and that there is potential for stimulation of their in situ growth and activity.
The nutritional responses of unattached and attached bacterial communities were studied in groundwater from 3 sampling depths, i.e., 830-841 m, 910-921 m, and 999-1,078 m, of the subvertical borehole KLX01 at the Laxemar study area in SE Sweden. The salinity profile of the groundwater in this borehole is homogeneous. There were negative redox potentials (Eh) in the waters (-220 to -270 mV) and they contained sulfide, hydrogen, and methane. Biofilm reactors with hydrophilic glass surfaces were connected to the flowing groundwaters from each of the 3 depths with flow rates of approximately 3 x 10(-3) m sec(-1) over 19 days. There were 0.15 to 0.68 × 10(5) unattached bacteria ml(-1) groundwater and 0.94 to 1.2 × 10(5) attached bacteria cm(-2) on the surfaces. The assimilations of (14)CO2, (14)C-formate, 1,2,3-(3)H-acetate, U-(14)C-lactate, U-(14)C-glucose, and L-4,5-(3)H-leucine by the communities were demonstrated with microautoradiographic and liquid scintillation counting techniques. There were significant assimilations of CO2 by all communities, except for the unattached bacteria at the 910-921 m depth, indicating in situ production of organic carbon from carbonate. Assimilation of formate was detected in two communities, indicating the presence of bacteria able to substitute CO2 with formate. Acetate, lactate, and glucose assimilations demonstrated the presence of heterotrophic bacteria. The assimilation of lactate by the attached bacteria dominated over acetate and glucose at all depths. Leucine was assimilated by 20 to 98% of the communities, which showed that major portions of the communities studied were viable. The results indicate that the attached communities at the 830-841 m and 910-921 m depths were in more metabolically active states than the unattached bacteria. Incubation in air compared with N2 indicated that portions of the studied communities were obligate anaerobes, as their ability to assimilate the added compounds was sensitive to oxygen. The results show that the use of several different compounds reduces the risk for false conclusions about the viability and the metabolic activity of the deep groundwater communities.
To characterize the deep subsurface environment of Rainier Mesa, Nevada Test Site, rock samples were taken from tunnels U 12b, U12g, U12p, and U 12n, which varied in depth from 50 m to 450 m and in gravimetric moisture content from 4% to 27%. Values for total count, viable count, biomass, Simpson diversity, equitability, similarity coefficient, and number of distinct colony types indicated microbiological variability between samples. Viable counts ranged from less than 1 × 10(1) to 2.4 × 10(5) CFU g dry wt(-1) of rock. Direct counts and enumeration based on phospholipid determination indicated larger numbers of cells g dry wt-1 of rock than viable counts. Simpson diversity indices, equitability, and numbers of distinct colony types varied from 3.00 to 8.05, 0.21 to 0.89, and 7 to 19, respectively, and indicated heterogeneity between samples. Each distinct morphotype was purified and characterized. Gram reaction, morphology, metal and antibiotic resistances, and metabolic activities of each isolate confirmed spatial variability among microbiota isolated from different locations. Most probable numbers of nitrifying, sulfur oxidizing, and sulfur-reducing bacteria were below the limit of detection in all samples, while the numbers of nitrogen fixing bacteria ranged from below the level of detection to 7.8 × 10(2) cells g dry wt(-1) of rock sample, and the numbers of dentrifying bacteria ranged from below the level of detection to greater than 1.6 × 10(3) cells g dry wt(-1) of rock sample.
The microbial diversity in two deep, confined aquifers, the Grande Ronde (1270 m) and the Priest Rapids (316 m), Hanford Reservation, Washington, USA, was investigated by sampling from artesian wells. These basaltic aquifers were alkaline (pH 8.5 to 10.5) and anaerobic (Eh -200 to -450 mV). The wells were allowed to free-flow until pH and Eh stabilized, then the microflora was sampled with water filtration and flow-through sandtrap methods. Direct microscopic counts showed 7.6 × 10(5) and 3.6 × 10(3) bacteria ml(-1) in water from the Grande Ronde and Priest Rapids aquifers, respectively. The sand filter method yielded 5.7 × 10(8) and 1.1 × 10(5) cells g(-1) wet weight of sand. The numbers of bacteria did not decrease as increasing volumes of water were flushed out. The heterotrophic diversity of these bacterial populations was assessed using enrichments for 20 functional groups. These groups were defined by their ability to grow in a matrix of five different electron acceptors (O2, Fe(III), NO3 (-), SO4 (2-), HCO3 (-)) and four groups of electron donors (fermentation products, monomers, polymers, aromatics) in a mineral salts medium at pH 9.5. Growth was assessed by protein production. Culture media were subsequently analyzed to determine substrate utilization patterns. Substrate utilization patterns proved to be more reliable indicators of the presence of a particular physiological group than was protein production. The sand-trap method obtained a greater diversity of bacteria than did water filtration, presumably by enriching the proportion of normally sessile bacteria relative to planktonic bacteria. Substrate utilization patterns were different for microflora from the two aquifers and corresponded to their different geochemistries. Activities in the filtered water enrichments more closely matched those predicted by aquifer geochemistry than did the sand-trap enrichments. The greatest activities were found in Fe(III)-reducing enrichments from both wells, SO4-reducing enrichments from the Grande Ronde aquifer, and methanogenic enrichments from the Priest Rapids aquifer. Organisms from these aquifers may be useful for high-pH bioremediation applications as well as production of biotechnological products. These organisms may also be useful for modeling potential reactions near buried concrete, as might be found in subsurface waste depositories.
Bacterial biomass was produced by culturing polysaccharide-producing Bacillus circulans in liquid medium containing glucose as carbon source. The biomass thus obtained was used to remove copper and cadmium ions from aqueous solutions. A biomass concentration of 1·48–1·52 g dry weight/l was found to remove 80% of copper and 44% of cadmium from solutions containing 495 ppm copper and 492 ppm cadmium, respectively. The pH of the metal solutions was found to have a pronounced effect on the metal-accumulating capacity of the organism. The removal of copper and cadmium ions from metal solutions by this bacterium was very efficient at low concentration ranges.
This paper presents a hypothesis on the importance of initial microbial adhesion in the overall process of biofilm formation. The hypothesis is based on the realization that dynamic shear conditions exist in many environments, such as in the oral cavity, or on rocks and ship hulls. Recognizing that an entire biofilm is detached during high shear once the bond between the initially adhering organisms and a surface (often constituted through a so-called ‘conditioning film’) is broken, it becomes clear that research should focus on detachment rather than adhesion. Experiments were done in a parallel plate flow chamber in which attempts were made to detach adhering oral streptococci from glass by applying a high shear caused by the passage of a bubble, giving an air-liquid interface. Detachment of streptococci from bare glass and from an initially adhering actinomycete strain appeared not to occur. However, substantial detachment of adhering streptococci occurred when adhesion was mediated through a salivary conditioning film, presumably because of cohesive failure in the conditioning film.
Bacterial communities were detected in deep crystalline rock aquifers within the Columbia River Basalt Group (CRB). CRB ground waters contained up to 60 {mu}M dissolved H{sub 2} and autotrophic microorganisms outnumbered heterotrophs. Stable carbon isotope measurements implied that autotrophic methanogenesis dominated this ecosystem and was coupled to the depletion of dissolved inorganic carbon. In laboratory experiments, H{sub 2} a potential energy source for bacteria, was produced by reactions between crushed basalt and anaerobic water. Microcosms containing only crushed basalt and ground water supported microbial growth. These results suggest that the CRB contains a lithoautotrophic microbial ecosystem that is independent of photosynthetic primary production. 38 refs., 4 figs., 3 tabs.
The microbially mediated oxidation of Ce(II1) and Mn(I1) in surface waters of Vineyard Sound, Mas- sachusetts, has been studied to evaluate the relationship between these two processes under different experimental conditions. These data, combined with earlier observations showing that Ce(II1) and Mn(I1) specific oxidation rates covary over a wide range of environments, suggest a close mechanistic relationship between the two processes which contributes to the marked similarities in the geochemistry of each element. Oxidation of Ce(II1) and Mn(I1) at different oxygen concentrations, pH, and concentrations of Mn(II), Ce(III), and Pr(II1) was studied with radiotracers. For both elements, oxidation was inhibited in the absence of oxygen. Ce(II1) oxidation was inhibited by Mn(I1) and vice versa, probably due to com- petitive inhibition within a common oxidative pathway. Pr(III), a nonredox analog of Ce(III), did not inhibit Mn(I1) oxidation nearly as effectively as Ce(II1) did, indicating that inhibition was not exclusively due to competition at a common binding site but that a redox step must also be involved. Both reactions exhibited a modest dependence on pH which was much smaller than would be expected for nonbiological oxidation. The results are consistent with a common oxidative pathway for Ce and Mn and indicate that an alternative process, nonbiological Ce oxidation on freshly formed Mn oxides, is unlikely. The results also illustrate the potential usefulness of Ce(II1) and Pr(II1) as probes of Mn uptake and redox transfor- mations in biological systems.
In order to more accurately predict the rates and mechanisms of radionuclide migration from low-level waste disposal facilities via groundwater transport, ongoing studies are being conducted at field sites at Chalk River Laboratories to identify and characterize the chemical speciation of mobile, long-lived radionuclides migrating in groundwaters. Large-volume water sampling techniques are being utilized to separate and concentrate radionuclides into particular, cationic, anionic, and nonionic chemical forms. Most radionuclides are migrating as soluble, anionic species that appear to be predominantly organoradionuclide complexes. Laboratory studies utilizing anion exchange chromatography have separated several anionically complexed radionuclides, e.g., â¶Â°Co and ¹°â¶Ru, into a number of specific compounds or groups of compounds. Further identification of the anionic organoradionuclide complexes is planned utilizing high resolution mass spectrometry. Large-volume ultra-filtration experiments are characterizing the particulate forms of radionuclides being transported in these groundwaters.
A mathematical model has been developed to study the migration of radionuclides through a single fracture from a high-level radioactive waste repository located in deep geological granite formations. The model utilizes two coupled equations; one for the fracture and the other for the host rock. The processes considered include advection, surface sorption, diffusive loss to the host rock and radioactive decay for transport in the fracture and radial diffusion, adsorption and radioactive decay for transport in the host rock. The source term to the model is provided as a two-component leach flux from the virtified waste form stored in the repository. The inlet concentration is derived using material balance for the amount of radioactivity that has entered into the fracture and host rock. Results indicate steep gradients in the radionuclide concentrations within the first 50 m along the fracture axis. It is observed that about 99% of the radioactivity is retained by the host rock. The radionuclide concentration in the fracture water increases as the fracture radius increases until a critical fracture radius is reached. Thereafter the concentration decreases due to the increase in the volumetric flux of water. The magnitude of the critical fracture radius mainly depends on the fracture water velocity.
The final microfora in the corrosion process of concrete sewer pipes was investigated. When the corroded sample was examined using several media, bacterial colonies were found only on acid media (pH 2.5); fungi were detected on neutral solid media (pH 6.5) as well as on acid media (pH 2.5). The acidophilic bacterial colonies were identified as Thiobacillus thiooxidans using a specific identification method for species of acidophilic thiobacilli. The dark green fungi that appeared on the isolation media showed similar morphological characteristics, even though the media used for isolation varied in pH and nutrient. The fungi showed tolerance against acid, although the optimum pH for their growth was neutral. The results showed that the severely corroded sewer pipe was inhabited by two kinds of microorganisms, Thiobacillus thiooxidans and the fungi. An isolated fungus, strain WSW, could oxidize sulfide to thiosulfate. Thiosulfate can be utilized by T. thiooxidans as an energy source, and is converted to corrosive sulfate. Continued vigorous growth of T. thiooxidans presumably depends on a mutualistic relationship with the fungus. It is proposed that a close association between the two microorganisms accelerates the corrosion of concrete sewer pipes.
Remediation of contaminated soil by inoculated bacteria requires movement of the bacteria to the site of contamination. However, the surface-inoculated pseudomonad mineralized little of the substrate present in the bottom 0.4-cm portion of nonsterile soil or aquifer sand that had been sterilized prior to inoculation, although mineralization occurred at the bottom of nonsterile aquifer sand. Little biodegradation was evident if the bacterium and the substrate were both at the bottom part of columns of soil and aquifer sand receiving intermittent flows of water, although rapid biodegradation occurred at this site in soil if the water flow was constant. We suggest that bacteria added to the soil surface or to aquifer solids for biodegradation may not be transported sufficiently to reach organic pollutants at sites distant from channels or macropores.
The influence of sulfate‐reducing bacteria on corrosion of mild steel is reviewed, with special emphasis on the effects of biofilm structure and function, medium composition (dissolved oxygen and ferrous ion concentrations) and the physical and chemical properties of iron sulfides. A summary of different corrosion mechanisms is critically discussed, based on electrochemical and rate process analyses. A mechanism is proposed which explains the high corrosion rates observed in the field.
The dissolution of several normal and inverse ferrites by Clostridium sp. under anaerobic conditions occurs through enzymatic reductive dissolution of iron (direct action) and through organic acid metabolites (indirect action) produced by the bacteria. The iron in the octahedral coordination in normal spinel and in tetrahe‐dral coordination with the divalent metal in inverse spinel was solubilized by direct action of the bacteria. Although the extent of dissolution of the ferrites differed, there was no clear relationship between the type of ferrite (normal and inverse spinels) and the mechanism of dissolution. The inverse spinels containing cobalt and copper ferrites were solubilized by indirect and direct action, respectively. Among the normal spinels tested, manganese ferrite was solubilized by direct action, while zinc ferrite was solubilized by direct and indirect action. Nickel ferrite was not solubilized by direct or indirect action. Cobalt, copper, manganese, nickel, and zinc ferrites had no effect on the growth of the bacteria. Dissolution of toxic metals and iron from fossil and nuclear energy wastes containing ferrite compounds by anaerobic microbial activity could be significant.
As part of a multidisciplinary project, microbiological studies were carried out on cores removed from aquifer sediment from three separate boreholes in the London Basin. This included an assessment of the number of aerobic heterotrophs and the ability to lower the redox potential, remove nitrate, and reduce sulfate in the presence of an organic substrate. The results demonstrated the presence of these bacteria and showed that the microbial potential varied with depth and between the boreholes. The level of water saturation of the sediments and the presence of available indigenous organic matter were factors determining the distribution of these microorganisms.
Subsurface sediment samples, collected from three boreholes ranging in depths from 0.1 to 260 m, were used in substrate mineralization studies to examine the aerobic metabolic potential of microbial populations indigenous to the deep subsurface. Mineralization was measured by quantifying the amount of CO2 released from radiolabeled acetate, phenol, or 4‐methoxybenzoate added to subsurface sediments at 10 μg g. Mineralization of the three compounds was observed in all but a few of the subsurface samples and did not decrease with depth. In addition, mineralization data collected from similar geologic formations from the different boreholes indicated that there was significant lateral continuity of microbial activity. Regression analyses were performed to determine which environmental factors were related to microbial metabolic potential. Mineralization was positively correlated with heterotrophic abundance as measured by plate counts. Other parameters that appeared to influence metabolic potential included pH and clay content.