Methane oxidation coupled to oxygenic photosynthesis in anoxic waters

PubMed Central

Milucka, Jana; Kirf, Mathias; Lu, Lu; Krupke, Andreas; Lam, Phyllis; Littmann, Sten; Kuypers, Marcel MM; Schubert, Carsten J

2015-01-01

Freshwater lakes represent large methane sources that, in contrast to the Ocean, significantly contribute to non-anthropogenic methane emissions to the atmosphere. Particularly mixed lakes are major methane emitters, while permanently and seasonally stratified lakes with anoxic bottom waters are often characterized by strongly reduced methane emissions. The causes for this reduced methane flux from anoxic lake waters are not fully understood. Here we identified the microorganisms and processes responsible for the near complete consumption of methane in the anoxic waters of a permanently stratified lake, Lago di Cadagno. Interestingly, known anaerobic methanotrophs could not be detected in these waters. Instead, we found abundant gamma-proteobacterial aerobic methane-oxidizing bacteria active in the anoxic waters. In vitro incubations revealed that, among all the tested potential electron acceptors, only the addition of oxygen enhanced the rates of methane oxidation. An equally pronounced stimulation was also observed when the anoxic water samples were incubated in the light. Our combined results from molecular, biogeochemical and single-cell analyses indicate that methane removal at the anoxic chemocline of Lago di Cadagno is due to true aerobic oxidation of methane fuelled by in situ oxygen production by photosynthetic algae. A similar mechanism could be active in seasonally stratified lakes and marine basins such as the Black Sea, where light penetrates to the anoxic chemocline. Given the widespread occurrence of seasonally stratified anoxic lakes, aerobic methane oxidation coupled to oxygenic photosynthesis might have an important but so far neglected role in methane emissions from lakes. PMID:25679533

Suitable flow pattern increases the removal efficiency of nitrogen in gravity sewers: a suitable anoxic and aerobic environment in biofilms.

PubMed

He, Qiang; Yin, Feixian; Li, Hong; Wang, Yinliang; Xu, Jingwei; Ai, Hainan

2018-03-25

The sewers have the function of carbon removal, which has been proven. But if the effect of nitrogen removal can be enhanced at the same time of carbon removal, it can lay a foundation for the realization of "sewer's working as a reactor." This paper investigated the effects of shear stress and C/N ratio on nitrogen removal through biofilms on the sewer inner wall and nitrogen transfer. The main conclusions are as follows: (1) nitrogen could be partially removed in sewers after a series of reactions; (2) the anaerobic, anoxic, aerobic environment and some bacteria related to nitrogen metabolism, which exist in the biofilm, promote the nitrification and denitrification; (3) a total of 722 functional genes involved in nitrogen metabolism were detected in the biofilm (C/N ratio of 10, shear stress of 1.4 Pa), accounting for 0.67% of all genes, and the functional genes related to denitrification were dominant. Graphical abstract ᅟ.

Cd Mobility in Anoxic Fe-Mineral-Rich Environments - Potential Use of Fe(III)-Reducing Bacteria in Soil Remediation

NASA Astrophysics Data System (ADS)

Muehe, E. M.; Adaktylou, I. J.; Obst, M.; Schröder, C.; Behrens, S.; Hitchcock, A. P.; Tylsizczak, T.; Michel, F. M.; Krämer, U.; Kappler, A.

2014-12-01

Agricultural soils are increasingly burdened with heavy metals such as Cd from industrial sources and impure fertilizers. Metal contaminants enter the food chain via plant uptake from soil and negatively affect human and environmental health. New remediation approaches are needed to lower soil metal contents. To apply these remediation techniques successfully, it is necessary to understand how soil microbes and minerals interact with toxic metals. Here we show that microbial Fe(III) reduction initially mobilizes Cd before its immobilization under anoxic conditions. To study how microbial Fe(III) reduction influences Cd mobility, we isolated a new Cd-tolerant, Fe(III)-reducing Geobacter sp. from a heavily Cd-contaminated soil. In lab experiments, this Geobacter strain first mobilized Cd from Cd-loaded Fe(III) hydroxides followed by precipitation of Cd-bearing mineral phases. Using Mössbauer spectroscopy and scanning electron microscopy, the original and newly formed Cd-containing Fe(II) and Fe(III) mineral phases, including Cd-Fe-carbonates, Fe-phosphates and Fe-(oxyhydr)oxides, were identified and characterized. Using energy-dispersive X-ray spectroscopy and synchrotron-based scanning transmission X-ray microscopy, Cd was mapped in the Fe(II) mineral aggregates formed during microbial Fe(III) reduction. Microbial Fe(III) reduction mobilizes Cd prior to its precipitation in Cd-bearing mineral phases. The mobilized Cd could be taken up by phytoremediating plants, resulting in a net removal of Cd from contaminated sites. Alternatively, Cd precipitation could reduce Cd bioavailability in the environment, causing less toxic effects to crops and soil microbiota. However, the stability and thus bioavailability of these newly formed Fe-Cd mineral phases needs to be assessed thoroughly. Whether phytoremediation or immobilization of Cd in a mineral with reduced Cd bioavailability are feasible mechanisms to reduce toxic effects of Cd in the environment remains to be

H2 cycling and microbial bioenergetics in anoxic sediments

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; DeVincenzi, Donald (Technical Monitor)

2001-01-01

The simple biochemistry of H2 is central to a large number of microbial processes, affecting the interaction of organisms with each other and with the environment. In anoxic sediments, the great majority of microbial redox processes involve H2 as a reactant, product, or potential by-product, and the thermodynamics of these processes are thus highly sensitive to fluctuations in environmental H2 concentrations. In turn, H2 concentrations are controlled by the activity of H2-consuming microorganisms, which efficiently utilize this substrate down to levels which correspond to their bioenergetic limitations. Consequently, any environmental change which impacts the thermodynamics of H2-consuming organisms is mirrored by a corresponding change in H2 concentrations. This phenomenon is illustrated in anoxic sediments from Cape Lookout Bight, NC, USA: H2 concentrations are controlled by a suite of environmental parameters (e.g., temperature, sulfate concentrations) in a fashion which can be quantitatively described by a simple thermodynamic model. These findings allow us to calculate the apparent minimum quantity of biologically useful energy in situ. We find that sulfate reducing bacteria are not active at energy yields below -18 kJ per mole sulfate, while methanogenic archaea exhibit a minimum close to -10 kJ per mole methane.

Source environment feature related phylogenetic distribution pattern of anoxygenic photosynthetic bacteria as revealed by pufM analysis.

PubMed

Zeng, Yonghui; Jiao, Nianzhi

2007-06-01

Anoxygenic photosynthesis, performed primarily by anoxygenic photosynthetic bacteria (APB), has been supposed to arise on Earth more than 3 billion years ago. The long established APB are distributed in almost every corner where light can reach. However, the relationship between APB phylogeny and source environments has been largely unexplored. Here we retrieved the pufM sequences and related source information of 89 pufM containing species from the public database. Phylogenetic analysis revealed that horizontal gene transfer (HGT) most likely occurred within 11 out of a total 21 pufM subgroups, not only among species within the same class but also among species of different phyla or subphyla. A clear source environment feature related phylogenetic distribution pattern was observed, with all species from oxic habitats and those from anoxic habitats clustering into independent subgroups, respectively. HGT among ancient APB and subsequent long term evolution and adaptation to separated niches may have contributed to the coupling of environment and pufM phylogeny.

Evolutionary and geologic consequences of organic carbon fixing in the primitive anoxic ocean

NASA Astrophysics Data System (ADS)

Berry, W. B. N.; Wilde, P.

1983-03-01

Steps leading to development of the modern photic-based marine food web are postulated as the result of modifications of the environment, enhanced by the activity of Archean sulfur chemoautotrophs. Such organisms (Anoxium) evolved in an anoxic ocean prior to 3.9 × 109 yr ago at Archean analogs of modern oceanic hydrothermal vents. At this time geothermal energy was more readily available to organisms than photic energy, given atmospheric conditions at the surface similar to Venus, where intensity is low and only middle and red visible wavelengths penetrate the cloudy CO2-rich atmosphere. Competition for the reduced sulfur developed due to oxidation and loss of sulfur to sediments. Consequently, evolutionary advantage shifted to Anoxium isolates that could use alternate energy sources such as light to supplement the diminished supplies of reduced sulfur. Initially, photo-sulfur organisms evolved similar to modern purple bacteria that absorb in the red visible spectra. Subsequent carbon fixing and oxidation improved both the quantity and range of light reaching the ocean surface. This permitted absorption in the blue visible range so that water splitting was now feasible, releasing free oxygen and accelerating oxidation. Eventually, reducing environments became restricted, completing the shift in the principal marine carbon-fixing activity from anoxic chemoautotrophic to aerobic photosynthetic organisms.

ACETOGENIC BACTERIA ASSOCIATED WITH SEAGRASS ROOTS

EPA Science Inventory

Seagrasses are adapted to being rooted in reduced, anoxic sediments with high rates of sulfate reduction. During the day, an oxygen gradient is generated around the roots, becoming anoxic at night. Thus, obligate anaerobic bacteria in the rhizosphere have to tolerate elevated oxy...

Cryptic oxygen cycling in anoxic marine zones

PubMed Central

Padilla, Cory C.; Stewart, Frank J.; Ulloa, Osvaldo; Paulmier, Aurélien; Gregori, Gerald; Revsbech, Niels Peter

2017-01-01

Oxygen availability drives changes in microbial diversity and biogeochemical cycling between the aerobic surface layer and the anaerobic core in nitrite-rich anoxic marine zones (AMZs), which constitute huge oxygen-depleted regions in the tropical oceans. The current paradigm is that primary production and nitrification within the oxic surface layer fuel anaerobic processes in the anoxic core of AMZs, where 30–50% of global marine nitrogen loss takes place. Here we demonstrate that oxygenic photosynthesis in the secondary chlorophyll maximum (SCM) releases significant amounts of O2 to the otherwise anoxic environment. The SCM, commonly found within AMZs, was dominated by the picocyanobacteria Prochlorococcus spp. Free O2 levels in this layer were, however, undetectable by conventional techniques, reflecting a tight coupling between O2 production and consumption by aerobic processes under apparent anoxic conditions. Transcriptomic analysis of the microbial community in the seemingly anoxic SCM revealed the enhanced expression of genes for aerobic processes, such as nitrite oxidation. The rates of gross O2 production and carbon fixation in the SCM were found to be similar to those reported for nitrite oxidation, as well as for anaerobic dissimilatory nitrate reduction and sulfate reduction, suggesting a significant effect of local oxygenic photosynthesis on Pacific AMZ biogeochemical cycling. PMID:28716941

Cryptic oxygen cycling in anoxic marine zones.

PubMed

Garcia-Robledo, Emilio; Padilla, Cory C; Aldunate, Montserrat; Stewart, Frank J; Ulloa, Osvaldo; Paulmier, Aurélien; Gregori, Gerald; Revsbech, Niels Peter

2017-08-01

Oxygen availability drives changes in microbial diversity and biogeochemical cycling between the aerobic surface layer and the anaerobic core in nitrite-rich anoxic marine zones (AMZs), which constitute huge oxygen-depleted regions in the tropical oceans. The current paradigm is that primary production and nitrification within the oxic surface layer fuel anaerobic processes in the anoxic core of AMZs, where 30-50% of global marine nitrogen loss takes place. Here we demonstrate that oxygenic photosynthesis in the secondary chlorophyll maximum (SCM) releases significant amounts of O 2 to the otherwise anoxic environment. The SCM, commonly found within AMZs, was dominated by the picocyanobacteria Prochlorococcus spp. Free O 2 levels in this layer were, however, undetectable by conventional techniques, reflecting a tight coupling between O 2 production and consumption by aerobic processes under apparent anoxic conditions. Transcriptomic analysis of the microbial community in the seemingly anoxic SCM revealed the enhanced expression of genes for aerobic processes, such as nitrite oxidation. The rates of gross O 2 production and carbon fixation in the SCM were found to be similar to those reported for nitrite oxidation, as well as for anaerobic dissimilatory nitrate reduction and sulfate reduction, suggesting a significant effect of local oxygenic photosynthesis on Pacific AMZ biogeochemical cycling.

Sodium lauryl ether sulfate (SLES) degradation by nitrate-reducing bacteria.

PubMed

Paulo, Ana M S; Aydin, Rozelin; Dimitrov, Mauricio R; Vreeling, Harm; Cavaleiro, Ana J; García-Encina, Pedro A; Stams, Alfons J M; Plugge, Caroline M

2017-06-01

The surfactant sodium lauryl ether sulfate (SLES) is widely used in the composition of detergents and frequently ends up in wastewater treatment plants (WWTPs). While aerobic SLES degradation is well studied, little is known about the fate of this compound in anoxic environments, such as denitrification tanks of WWTPs, nor about the bacteria involved in the anoxic biodegradation. Here, we used SLES as sole carbon and energy source, at concentrations ranging from 50 to 1000 mg L -1 , to enrich and isolate nitrate-reducing bacteria from activated sludge of a WWTP with the anaerobic-anoxic-oxic (A 2 /O) concept. In the 50 mg L -1 enrichment, Comamonas (50%), Pseudomonas (24%), and Alicycliphilus (12%) were present at higher relative abundance, while Pseudomonas (53%) became dominant in the 1000 mg L -1 enrichment. Aeromonas hydrophila strain S7, Pseudomonas stutzeri strain S8, and Pseudomonas nitroreducens strain S11 were isolated from the enriched cultures. Under denitrifying conditions, strains S8 and S11 degraded 500 mg L -1 SLES in less than 1 day, while strain S7 required more than 6 days. Strains S8 and S11 also showed a remarkable resistance to SLES, being able to grow and reduce nitrate with SLES concentrations up to 40 g L -1 . Strain S11 turned out to be the best anoxic SLES degrader, degrading up to 41% of 500 mg L -1 . The comparison between SLES anoxic and oxic degradation by strain S11 revealed differences in SLES cleavage, degradation, and sulfate accumulation; both ester and ether cleavage were probably employed in SLES anoxic degradation by strain S11.

Isolation of Acetogenic Bacteria That Induce Biocorrosion by Utilizing Metallic Iron as the Sole Electron Donor

PubMed Central

Yumoto, Isao; Kamagata, Yoichi

2014-01-01

Corrosion of iron occurring under anoxic conditions, which is termed microbiologically influenced corrosion (MIC) or biocorrosion, is mostly caused by microbial activities. Microbial activity that enhances corrosion via uptake of electrons from metallic iron [Fe(0)] has been regarded as one of the major causative factors. In addition to sulfate-reducing bacteria and methanogenic archaea in marine environments, acetogenic bacteria in freshwater environments have recently been suggested to cause MIC under anoxic conditions. However, no microorganisms that perform acetogenesis-dependent MIC have been isolated or had their MIC-inducing mechanisms characterized. Here, we enriched and isolated acetogenic bacteria that induce iron corrosion by utilizing Fe(0) as the sole electron donor under freshwater, sulfate-free, and anoxic conditions. The enriched communities produced significantly larger amounts of Fe(II) than the abiotic controls and produced acetate coupled with Fe(0) oxidation prior to CH4 production. Microbial community analysis revealed that Sporomusa sp. and Desulfovibrio sp. dominated in the enrichments. Strain GT1, which is closely related to the acetogen Sporomusa sphaeroides, was eventually isolated from the enrichment. Strain GT1 grew acetogenetically with Fe(0) as the sole electron donor and enhanced iron corrosion, which is the first demonstration of MIC mediated by a pure culture of an acetogen. Other well-known acetogenic bacteria, including Sporomusa ovata and Acetobacterium spp., did not grow well on Fe(0). These results indicate that very few species of acetogens have specific mechanisms to efficiently utilize cathodic electrons derived from Fe(0) oxidation and induce iron corrosion. PMID:25304512

Isolation of acetogenic bacteria that induce biocorrosion by utilizing metallic iron as the sole electron donor.

PubMed

Kato, Souichiro; Yumoto, Isao; Kamagata, Yoichi

2015-01-01

Corrosion of iron occurring under anoxic conditions, which is termed microbiologically influenced corrosion (MIC) or biocorrosion, is mostly caused by microbial activities. Microbial activity that enhances corrosion via uptake of electrons from metallic iron [Fe(0)] has been regarded as one of the major causative factors. In addition to sulfate-reducing bacteria and methanogenic archaea in marine environments, acetogenic bacteria in freshwater environments have recently been suggested to cause MIC under anoxic conditions. However, no microorganisms that perform acetogenesis-dependent MIC have been isolated or had their MIC-inducing mechanisms characterized. Here, we enriched and isolated acetogenic bacteria that induce iron corrosion by utilizing Fe(0) as the sole electron donor under freshwater, sulfate-free, and anoxic conditions. The enriched communities produced significantly larger amounts of Fe(II) than the abiotic controls and produced acetate coupled with Fe(0) oxidation prior to CH4 production. Microbial community analysis revealed that Sporomusa sp. and Desulfovibrio sp. dominated in the enrichments. Strain GT1, which is closely related to the acetogen Sporomusa sphaeroides, was eventually isolated from the enrichment. Strain GT1 grew acetogenetically with Fe(0) as the sole electron donor and enhanced iron corrosion, which is the first demonstration of MIC mediated by a pure culture of an acetogen. Other well-known acetogenic bacteria, including Sporomusa ovata and Acetobacterium spp., did not grow well on Fe(0). These results indicate that very few species of acetogens have specific mechanisms to efficiently utilize cathodic electrons derived from Fe(0) oxidation and induce iron corrosion. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Effect of nitrate concentration on filamentous bulking under low level of dissolved oxygen in an airlift inner circular anoxic-aerobic incorporate reactor.

PubMed

Su, Yiming; Zhang, Yalei; Zhou, Xuefei; Jiang, Ming

2013-09-01

This laboratory research investigated a possible cause of filamentous bulking under low level of dissolved oxygen conditions (dissolved oxygen value in aerobic zone maintained between 0.6-0.8 mg O2/L) in an airlift inner-circular anoxic-aerobic reactor. During the operating period, it was observed that low nitrate concentrations affected sludge volume index significantly. Unlike the existing hypothesis, the batch tests indicated that filamentous bacteria (mainly Thiothrix sp.) could store nitrate temporarily under carbon restricted conditions. When nitrate concentration was below 4 mg/L, low levels of carbon substrates and dissolved oxygen in the aerobic zone stimulated the nitrate-storing capacity of filaments. When filamentous bacteria riched in nitrate reached the anoxic zone, where they were exposed to high levels of carbon but limited nitrate, they underwent denitrification. However, when nonfilamentous bacteria were exposed to similar conditions, denitrification was restrained due to their intrinsic nitrate limitation. Hence, in order to avoid filamentous bulking, the nitrate concentration in the return sludge (from aerobic zone to the anoxic zone) should be above 4 mg/L, or alternatively, the nitrate load in the anoxic zone should be kept at levels above 2.7 mg NO(3-)-N/g SS.

Anaerobic degradation of benzene in diverse anoxic environments

USGS Publications Warehouse

Kazumi, J.; Caldwell, M.E.; Suflita, J.M.; Lovely, D.R.; Young, L.Y.

1997-01-01

Benzene has often been observed to be resistant to microbial degradation under anoxic conditions. A number of recent studies, however, have demonstrated that anaerobic benzene utilization can occur. This study extends the previous reports of anaerobic benzene degradation to sediments that varied with respect to contamination input, predominant redox condition, and salinity. In spite of differences in methodology, microbial degradation of benzene was noted in slurries constructed with sediments from various geographical locations and range from aquifer sands to fine-grained estuarine muds, under methanogenic, sulfate-reducing, and iron-reducing conditions. In aquifer sediments under methanogenic conditions, benzene loss was concomitant with methane production, and microbial utilization of [14C]benzene yielded 14CO2 and 14CH4. In slurries with estuarine and aquifer sediments under sulfate-reducing conditions, the loss of sulfate in amounts consistent with the stoichiometric degradation of benzene or the conversion of [14C]benzene to 14CO2 indicates that benzene was mineralized. Benzene loss also occurred in the presence of Fe(III) in sediments from freshwater environments. Microbial benzene utilization, however, was not observed under denitrifying conditions. These results indicate that the potential for the anaerobic degradation of benzene, which was once thought to be resistant to non-oxygenase attack, exists in a variety of aquatic sediments from widely distributed locations.

Understanding the Dynamics of the Oxic-Anoxic Interface in the Black Sea

NASA Astrophysics Data System (ADS)

Stanev, Emil V.; Poulain, Pierre-Marie; Grayek, Sebastian; Johnson, Kenneth S.; Claustre, Hervé; Murray, James W.

2018-01-01

The Black Sea, the largest semienclosed anoxic basin on Earth, can be considered as an excellent natural laboratory for oxic and anoxic biogeochemical processes. The suboxic zone, a thin interface between oxic and anoxic waters, still remains poorly understood because it has been undersampled. This has led to alternative concepts regarding the underlying processes that create it. Existing hypotheses suggest that the interface originates either by isopycnal intrusions that introduce oxygen or the dynamics of manganese redox cycling that are associated with the sinking of particles or chemosynthetic bacteria. Here we reexamine these concepts using high-resolution oxygen, sulfide, nitrate, and particle concentration profiles obtained with sensors deployed on profiling floats. Our results show an extremely stable structure in density space over the entire basin with the exception of areas near the Bosporus plume and in the southern areas dominated by coastal anticyclones. The absence of large-scale horizontal intrusive signatures in the open-sea supports a hypothesis prioritizing the role of biogeochemical processes.

Cable Bacteria in Freshwater Sediments

PubMed Central

Kristiansen, Michael; Frederiksen, Rasmus B.; Dittmer, Anders Lindequist; Bjerg, Jesper Tataru; Trojan, Daniela; Schreiber, Lars; Damgaard, Lars Riis; Schramm, Andreas; Nielsen, Lars Peter

2015-01-01

In marine sediments cathodic oxygen reduction at the sediment surface can be coupled to anodic sulfide oxidation in deeper anoxic layers through electrical currents mediated by filamentous, multicellular bacteria of the Desulfobulbaceae family, the so-called cable bacteria. Until now, cable bacteria have only been reported from marine environments. In this study, we demonstrate that cable bacteria also occur in freshwater sediments. In a first step, homogenized sediment collected from the freshwater stream Giber Å, Denmark, was incubated in the laboratory. After 2 weeks, pH signatures and electric fields indicated electron transfer between vertically separated anodic and cathodic half-reactions. Fluorescence in situ hybridization revealed the presence of Desulfobulbaceae filaments. In addition, in situ measurements of oxygen, pH, and electric potential distributions in the waterlogged banks of Giber Å demonstrated the presence of distant electric redox coupling in naturally occurring freshwater sediment. At the same site, filamentous Desulfobulbaceae with cable bacterium morphology were found to be present. Their 16S rRNA gene sequence placed them as a distinct sister group to the known marine cable bacteria, with the genus Desulfobulbus as the closest cultured lineage. The results of the present study indicate that electric currents mediated by cable bacteria could be important for the biogeochemistry in many more environments than anticipated thus far and suggest a common evolutionary origin of the cable phenotype within Desulfobulbaceae with subsequent diversification into a freshwater and a marine lineage. PMID:26116678

Microbial oxidative stress response: Novel insights from environmental facultative anaerobic bacteria.

PubMed

Fu, Huihui; Yuan, Jie; Gao, Haichun

2015-10-15

Facultative bacteria can grow under either oxic or anoxic conditions. While oxygen provides substantial advantages in energy yield by respiration, it can become life-threatening because of reactive oxygen species that derive from the molecule naturally. Thus, to survive and thrive in a given niche, these bacteria have to constantly regulate physiological processes to make maximum benefits from oxygen respiration while restraining oxidative stress. Molecular mechanisms and physiological consequences of oxidative stress have been under extensive investigation for decades, mostly on research model Escherichia coli, from which our understanding of bacterial oxidative stress response is largely derived. Nevertheless, given that bacteria live in enormously diverse environments, to cope with oxidative stress different strategies are conceivably developed. Copyright © 2015 Elsevier Inc. All rights reserved.

Methane production and simultaneous sulphate reduction in anoxic, salt marsh sediments

USGS Publications Warehouse

Oremland, R.S.; Marsh, L.M.; Polcin, S.

1982-01-01

It has been generally believed that sulphate reduction precludes methane generation during diagenesis of anoxic sediments1,2. Because most biogenic methane formed in nature is thought to derive either from acetate cleavage or by hydrogen reduction of carbon dioxide3-6, the removal of these compounds by the energetically more efficient sulphate-reducing bacteria can impose a substrate limitation on methanogenic bacteria 7-9. However, two known species of methanogens, Methanosarcina barkeri and Methanococcus mazei, can grow on and produce methane from methanol and methylated amines10-13. In addition, these compounds stimulate methane production by bacterial enrichments from the rumen11,14 and aquatic muds13,14. Methanol can enter anaerobic food webs through bacterial degradation of lignins15 or pectin16, and methylated amines can be produced either from decomposition of substances like choline, creatine and betaine13,14 or by bacterial reduction of trimethylamine oxide17, a common metabolite and excretory product of marine animals. However, the relative importance of methanol and methylated amines as precursors of methane in sediments has not been previously examined. We now report that methanol and trimethylamine are important substrates for methanogenic bacteria in salt marsh sediments and that these compounds may account for the bulk of methane produced therein. Furthermore, because these compounds do not stimulate sulphate reduction, methanogenesis and sulphate reduction can operate concurrently in sulphate-containing anoxic sediments. ?? 1982 Nature Publishing Group.

Oceanic oxygenation events in the anoxic Ediacaran ocean.

PubMed

Sahoo, S K; Planavsky, N J; Jiang, G; Kendall, B; Owens, J D; Wang, X; Shi, X; Anbar, A D; Lyons, T W

2016-09-01

The ocean-atmosphere system is typically envisioned to have gone through a unidirectional oxygenation with significant oxygen increases in the earliest (ca. 635 Ma), middle (ca. 580 Ma), or late (ca. 560 Ma) Ediacaran Period. However, temporally discontinuous geochemical data and the patchy metazoan fossil record have been inadequate to chart the details of Ediacaran ocean oxygenation, raising fundamental debates about the timing of ocean oxygenation, its purported unidirectional rise, and its causal relationship, if any, with the evolution of early animal life. To better understand the Ediacaran ocean redox evolution, we have conducted a multi-proxy paleoredox study of a relatively continuous, deep-water section in South China that was paleogeographically connected with the open ocean. Iron speciation and pyrite morphology indicate locally euxinic (anoxic and sulfidic) environments throughout the Ediacaran in this section. In the same rocks, redox sensitive element enrichments and sulfur isotope data provide evidence for multiple oceanic oxygenation events (OOEs) in a predominantly anoxic global Ediacaran-early Cambrian ocean. This dynamic redox landscape contrasts with a recent view of a redox-static Ediacaran ocean without significant change in oxygen content. The duration of the Ediacaran OOEs may be comparable to those of the oceanic anoxic events (OAEs) in otherwise well-oxygenated Phanerozoic oceans. Anoxic events caused mass extinctions followed by fast recovery in biologically diversified Phanerozoic oceans. In contrast, oxygenation events in otherwise ecologically monotonous anoxic Ediacaran-early Cambrian oceans may have stimulated biotic innovations followed by prolonged evolutionary stasis. © 2016 John Wiley & Sons Ltd.

Enhanced nitrogen removal from electroplating tail wastewater through two-staged anoxic-oxic (A/O) process.

PubMed

Yan, Xinmei; Zhu, Chunyan; Huang, Bin; Yan, Qun; Zhang, Guangsheng

2018-01-01

Consisted of anaerobic (ANA), anoxic-1 (AN1), aerobic-1 (AE1), anoxic-2 (AN2), aerobic-2 (AE2) reactors and sediment tank, the two-staged A/O process was applied for depth treatment of electroplating tail wastewater with high electrical conductivity and large amounts of ammonia nitrogen. It was found that the NH 4 + -N and COD removal efficiencies reached 97.11% and 83.00%, respectively. Besides, the short-term salinity shock of the control, AE1 and AE2 indicated that AE1 and AE2 have better resistance to high salinity when the concentration of NaCl ranged from 1 to 10g/L. Meanwhile, it was found through high-throughput sequencing that bacteria genus Nitrosomonas, Nitrospira and Thauera, which are capable of nitrogen removal, were enriched in the two-staged A/O process. Moreover, both salt-tolerant bacteria and halophili bacteria were also found in the combined process. Therefore, microbial community within the two-staged A/O process could be acclimated to high electrical conductivity, and adapted for electroplating tail wastewater treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Anaerobic animals from an ancient, anoxic ecological niche.

PubMed

Mentel, Marek; Martin, William

2010-04-06

Tiny marine animals that complete their life cycle in the total absence of light and oxygen are reported by Roberto Danovaro and colleagues in this issue of BMC Biology. These fascinating animals are new members of the phylum Loricifera and possess mitochondria that in electron micrographs look very much like hydrogenosomes, the H2-producing mitochondria found among several unicellular eukaryotic lineages. The discovery of metazoan life in a permanently anoxic and sulphidic environment provides a glimpse of what a good part of Earth's past ecology might have been like in 'Canfield oceans', before the rise of deep marine oxygen levels and the appearance of the first large animals in the fossil record roughly 550-600 million years ago. The findings underscore the evolutionary significance of anaerobic deep sea environments and the anaerobic lifestyle among mitochondrion-bearing cells. They also testify that a fuller understanding of eukaryotic and metazoan evolution will come from the study of modern anoxic and hypoxic habitats.

Anaerobic animals from an ancient, anoxic ecological niche

PubMed Central

2010-01-01

Tiny marine animals that complete their life cycle in the total absence of light and oxygen are reported by Roberto Danovaro and colleagues in this issue of BMC Biology. These fascinating animals are new members of the phylum Loricifera and possess mitochondria that in electron micrographs look very much like hydrogenosomes, the H2-producing mitochondria found among several unicellular eukaryotic lineages. The discovery of metazoan life in a permanently anoxic and sulphidic environment provides a glimpse of what a good part of Earth's past ecology might have been like in 'Canfield oceans', before the rise of deep marine oxygen levels and the appearance of the first large animals in the fossil record roughly 550-600 million years ago. The findings underscore the evolutionary significance of anaerobic deep sea environments and the anaerobic lifestyle among mitochondrion-bearing cells. They also testify that a fuller understanding of eukaryotic and metazoan evolution will come from the study of modern anoxic and hypoxic habitats. PMID:20370917

Anaerobic/oxic/anoxic granular sludge process as an effective nutrient removal process utilizing denitrifying polyphosphate-accumulating organisms.

PubMed

Kishida, Naohiro; Kim, Juhyun; Tsuneda, Satoshi; Sudo, Ryuichi

2006-07-01

In a biological nutrient removal (BNR) process, the utilization of denitrifying polyphosphate-accumulating organisms (DNPAOs) has many advantages such as effective use of organic carbon substrates and low sludge production. As a suitable process for the utilization of DNPAOs in BNR, an anaerobic/oxic/anoxic granular sludge (AOAGS) process was proposed in this study. In spite of performing aeration for nitrifying bacteria, the AOAGS process can create anaerobic/anoxic conditions suitable for the cultivation of DNPAOs because anoxic zones exist inside the granular sludge in the oxic phase. Thus, DNPAOs can coexist with nitrifying bacteria in a single reactor. In addition, the usability of DNPAOs in the reactor can be improved by adding the anoxic phase after the oxic phase. These characteristics enable the AOAGS process to attain effective removal of both nitrogen and phosphorus. When acetate-based synthetic wastewater (COD: 600 mg/L, NH4-N: 60 mg/L, PO(4)-P: 10 mg/L) was supplied to a laboratory-scale sequencing batch reactor under the operation of anaerobic/oxic/anoxic cycles, granular sludge with a diameter of 500 microm was successfully formed within 1 month. Although the removal of both nitrogen and phosphorus was almost complete at the end of the oxic phase, a short anoxic period subsequent to the oxic phase was necessary for further removal of nitrogen and phosphorus. As a result, effluent concentrations of NH(4)-N, NO(x)-N and PO(4)-P were always lower than 1 mg/L. It was found that penetration depth of oxygen inside the granular sludge was approximately 100 microm by microsensor measurements. In addition, from the microbiological analysis by fluorescence in situ hybridization, existence depth of polyphosphate-accumulating organisms was further than the maximum oxygen penetration depth. The water quality data, oxygen profiles and microbial community structure demonstrated that DNPAOs inside the granular sludge may be responsible for denitrification in the

Cultivation, detection, and ecophysiology of anaerobic ammonium-oxidizing bacteria.

PubMed

Kartal, Boran; Geerts, Wim; Jetten, Mike S M

2011-01-01

Anaerobic ammonium-oxidizing (anammox) bacteria oxidize ammonium with nitrite under anoxic conditions. The anammox process is currently used to remove ammonium from wastewater and contributes significantly to the loss of fixed nitrogen from the oceans. In this chapter, we focus on the ecophysiology of anammox bacteria and describe new methodologies to grow these microorganisms. Now, it is possible to enrich anammox bacteria up to 95% with a membrane bioreactor that removes forces of selection for fast settling aggregates and facilitates the growth of planktonic cells. The biomass from this system has a high anaerobic ammonium oxidation rate (50 fmol NH(4)(+) · cell(-1) day(-1)) and is suitable for many ecophysiological and molecular experiments. A high throughput Percoll density gradient centrifugation protocol may be applied on this biomass for further enrichment (>99.5%) of anammox bacteria. Furthermore, we provide an up-to-date list of commonly used primers and introduce protocols for quantification and detection of functional genes of anammox bacteria in their natural environment. Copyright © 2011 Elsevier Inc. All rights reserved.

[Anoxic bioremediation of urban polluted river water with biofilm].

PubMed

Zhang, Yong-Ming; Hu, Yi-Zhen; Yan, Rong; Liu, Fang

2009-07-15

Reactor like oxidation ditch was used for anaerobic bioremediation of urban river water, in which biofilm formed on ceramic honeycomb carrier was used instated of activated sludge. The dissolved oxygen in the wastewater was controlled under 0.5 mg/L for anoxic oxidation, and ammonia nitrogen was removed 40 to 60 percent, and total nitrogen removed 40 to 45 percent, that is ammonia nitrogen and total nitrogen were removed at the same time, also, nitrite was not any accumulated during the process. The biofilm was taken into flask to culture under anoxic oxidation condition in order to prove if anaerobic ammonium oxidation (ANAMMOX) occurred in the process, and ammonia and nitrite nitrogen were also removed at the same time in the experiment, which suggested that nitrification-denitrification and ANAMMOX occurred in bioremediation of urban surface water with low ratio of carbon and nitrogen at the same time. The anammox bacteria were existed in the biofilm according to molecular biological analysis. The experiment will be significant for bioremediation of eutrophication water body.

Complete nitrogen removal from municipal wastewater via partial nitrification by appropriately alternating anoxic/aerobic conditions in a continuous plug-flow step feed process.

PubMed

Ge, Shijian; Peng, Yongzhen; Qiu, Shuang; Zhu, Ao; Ren, Nanqi

2014-05-15

This study assessed the technical feasibility of removing nitrogen from municipal wastewater by partial nitrification (nitritation) in a continuous plug-flow step feed process. Nitrite in the effluent accumulated to over 81.5  ± 9.2% but disappeared with the transition of process operation from anoxic/oxic mode to the anaerobic/anoxic/oxic mode. Batch tests showed obvious ammonia oxidizing bacteria (AOB) stimulation (advanced ammonia oxidation rate) and nitrite (NOB) oxidizing bacteria inhibition (reduced nitrite oxidation rate) under transient anoxic conditions. Two main factors contributed to nitritation in this continuous plug-flow process: One was the alternating anoxic and oxic operational condition; the step feed strategy guaranteed timely denitrification in anoxic zones, allowing a reduction in energy supply (nitrite) to NOB. Fluorescence in Situ Hybridization and quantitative real-time polymerase chain reaction analysis indicated that NOB population gradually decreased to 1.0  ± 0.1% of the total bacterial population (dominant Nitrospira spp., 1.55 × 10(9) copies/L) while AOB increased approximately two-fold (7.4  ± 0.9%, 1.25 × 10(10) copies/L) during the above anoxic to anaerobic transition. Most importantly, without addition of external carbon sources, the above wastewater treatment process reached 86.0  ± 4.2% of total nitrogen (TN) removal with only 7.23 ± 2.31 mg/L of TN in the effluent, which met the discharge requirements. Copyright © 2014 Elsevier Ltd. All rights reserved.

Ecology and Biotechnology of Selenium-Respiring Bacteria

PubMed Central

2015-01-01

SUMMARY In nature, selenium is actively cycled between oxic and anoxic habitats, and this cycle plays an important role in carbon and nitrogen mineralization through bacterial anaerobic respiration. Selenium-respiring bacteria (SeRB) are found in geographically diverse, pristine or contaminated environments and play a pivotal role in the selenium cycle. Unlike its structural analogues oxygen and sulfur, the chalcogen selenium and its microbial cycling have received much less attention by the scientific community. This review focuses on microorganisms that use selenate and selenite as terminal electron acceptors, in parallel to the well-studied sulfate-reducing bacteria. It overviews the significant advancements made in recent years on the role of SeRB in the biological selenium cycle and their ecological role, phylogenetic characterization, and metabolism, as well as selenium biomineralization mechanisms and environmental biotechnological applications. PMID:25631289

Anoxic atmospheres on Mars driven by volcanism: Implications for past environments and life

NASA Astrophysics Data System (ADS)

Sholes, Steven F.; Smith, Megan L.; Claire, Mark W.; Zahnle, Kevin J.; Catling, David C.

2017-07-01

Mars today has no active volcanism and its atmosphere is oxidizing, dominated by the photochemistry of CO2 and H2O. Mars experienced widespread volcanism in the past and volcanic emissions should have included reducing gases, such as H2 and CO, as well as sulfur-bearing gases. Using a one-dimensional photochemical model, we consider whether plausible volcanic gas fluxes could have switched the redox-state of the past martian atmosphere to reducing conditions. In our model, the total quantity and proportions of volcanic gases depend on the water content, outgassing pressure, and oxygen fugacity of the source melt. We find that, with reasonable melt parameters, the past martian atmosphere (∼3.5 Gyr to present) could have easily reached reducing and anoxic conditions with modest levels of volcanism, >0.14 km3 yr-1, which are well within the range of estimates from thermal evolution models or photogeological studies. Counter-intuitively we also find that more reducing melts with lower oxygen fugacity require greater amounts of volcanism to switch a paleo-atmosphere from oxidizing to reducing. The reason is that sulfur is more stable in such melts and lower absolute fluxes of sulfur-bearing gases more than compensate for increases in the proportions of H2 and CO. These results imply that ancient Mars should have experienced periods with anoxic and reducing atmospheres even through the mid-Amazonian whenever volcanic outgassing was sustained at sufficient levels. Reducing anoxic conditions are potentially conducive to the synthesis of prebiotic organic compounds, such as amino acids, and are therefore relevant to the possibility of life on Mars. Also, anoxic reducing conditions should have influenced the type of minerals that were formed on the surface or deposited from the atmosphere. We suggest looking for elemental polysulfur (S8) as a signature of past reducing atmospheres. Finally, our models allow us to estimate the amount of volcanically sourced atmospheric

Characterization and mitigation of nitrous oxide (N2 O) emissions from partial and full-nitrification BNR processes based on post-anoxic aeration control.

PubMed

Brotto, Ariane Coelho; Li, Huosheng; Dumit, Muriel; Gabarró, Jordi; Colprim, Jesús; Murthy, Sudhir; Chandran, Kartik

2015-11-01

It has been reported that a directional change from anoxic to aerobic conditions is a common trigger for nitrous oxide (N2 O) production by ammonia oxidizing bacteria (AOB). By extension, during anoxic-aerobic cycling, post-anoxic dissolved oxygen (DO) concentrations might likely play a role in the magnitude of N2 O emissions observed. The overall goal of this study was to determine the impact of three select post-anoxic DO concentrations (0.8, 2.0, and 3.0 mg O2 /L) on N2 O emissions from partial-nitrification (PN) and full-nitrification (FN) reactors subjected to anoxic-aerobic cycling and, ultimately, to explore the development of strategies to minimize N2 O emissions from PN and FN based biological nitrogen removal (BNR) processes. Statistically similar N2 O emissions were observed during anoxia for both PN (0.62 ± 0.21% N load) and FN (0.61 ± 0.070% N load) processes. In contrast, N2 O emissions were statistically lower for PN (0.86 ± 0.25% N load) than for FN (4.6 ± 2.8% N load), during the post-anoxic aerobic phase, when compared together for all three post-anoxic DO concentrations. Further, for PN, the highest N2 O emissions were observed at the highest post-anoxic DO concentration of 3.0 mg O2 /L (1.2% N load), likely due to the highest corresponding AOB specific growth rate. In contrast, for FN, the highest N2 O emissions were at the lowest post-anoxic DO concentration of 0.8 mg O2 /L (8.5% N load). The higher emissions from FN process at low DO concentrations were associated with a lag in nitrite oxidizing bacteria activity upon recovery to aerobic conditions. This lag phase contributed to transient nitrite accumulation, and in turn correlated positively to the observed N2 O emissions. Based on our findings, a gradual ramp up in post-anoxic DO concentrations can minimize N2 O emissions during PN-based BNR, whereas a completely different strategy, entailing a rapid increase in post-anoxic DO concentrations can minimize

Natural attenuation potential of phenylarsenicals in anoxic groundwaters.

PubMed

Hempel, Michael; Daus, Birgit; Vogt, Carsten; Weiss, Holger

2009-09-15

The extensive production of chemical warfare agents in the 20th century has led to serious contamination of soil and groundwater with phenyl arsenicals at former ammunition depots or warfare agent production sites worldwide. Most phenyl arsenicals are highly toxic for humans. The microbial degradation of phenylarsonic acid (PAA) and diphenylarsinic acid (DPAA) was investigated in microcosms made of anoxic groundwater/sediment mixtures taken from different depths of an anoxic, phenyl arsenical contaminated aquifer in Central Germany. DPAA was not transformed within 91 days incubation time in any of the microcosms. The removal of PAA can be described by a first order kinetics without a lag-phase (rate: 0.037 d(-1)). In sterilized microcosms, PAA concentrations always remained stable, demonstrating that PAA transformation was a biologically mediated process. PAA transformation occurred under sulfate-reducing conditions due to sulfate consumption and production of sulfide. The addition of lactate (1 mM), a typical substrate of sulfate-reducing bacteria, increased the transformation rate of PAA significantly up to 0.134 d(-1). The content of total arsenic was considerably reduced (> 75%). Intermediates of PAA transformation were detected by high performance liquid chromatography-inductively coupled plasma mass spectrometry (HPLC-ICP-MS). Experiments with a pure strain and sterile controls of Desulfovibrio gigas spiked with PAA showed that the elimination process is linked to the presence of sulfide formed through bacterial activity. Phenyl arsenicals were likely immobilized in the sedimentthrough sulfur substitution and a subsequent sulfur bond under the prevailing sulfate reducing condition. The results of this study indicate that PAA can undergo microbiologically mediated transformation in anoxic aquifers, leading to reduced concentrations in groundwater, which indicate a (enhancend) natural attenuation potential.

Uranium and plutonium in anoxic marine sediments of the Santiago River mouth (Eastern Pacific, Mexico).

PubMed

Almazán-Torres, María Guadalupe; Ordóñez-Regil, Eduardo; Ruiz-Fernández, Ana Carolina

2016-11-01

The uranium (U) and plutonium (Pu) content with depth in a sediment core collected in the continental shelf off the mouth of the Santiago River in the Mexican Pacific was studied to evaluate the contamination effects of the effluent of the Santiago-Lerma River as it moves into the sea. The large mass of terrestrial detritus delivered by the river influences the physicochemical and geochemical processes in the seafloor. Abnormal concentrations of U and Pu in sediments were examined as indicative of the effects of anoxic conditions. One of the indicators of pollution of seawater is the bacterial activity of the shallow seabed layer; and among the prevailing bacteria, the magnetotactic ones induce the formation of euhedral and framboidal shapes (pyrite). These pyrite entities are by-products of anoxic environments loaded with decomposing detrital material and are very abundant in the surface layers of the sediment core analyzed. The pyrite formation is the result of a biochemical reaction between iron and organic sulphur reduced by bacteria, and the pyrite entities precipitate to the seafloor. In the same upper zone of the profile, 238 U is readily immobilized, while 234 U is oxidized and dissolved in seawater by the effect of hot atom chemistry. This may cause the activity ratio (AR) 234 U/ 238 U disequilibrium (near 0.41). Furthermore, in the shallow layer of the sediment core, an abnormally high concentration of 239+240 Pu was detected. In this upper layer, the activity concentrations found were 3.19 Bq kg -1 for 238 U, 1.32 kg -1 for 234 U and 2.78 Bq kg -1 for 239+240 Pu. In the lower fractions of the sediment core, normal values of AR 234 U/ 238 U (≈1) were found, with traces of 239+240 Pu. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ecology and biotechnology of selenium-respiring bacteria.

PubMed

Nancharaiah, Y V; Lens, P N L

2015-03-01

In nature, selenium is actively cycled between oxic and anoxic habitats, and this cycle plays an important role in carbon and nitrogen mineralization through bacterial anaerobic respiration. Selenium-respiring bacteria (SeRB) are found in geographically diverse, pristine or contaminated environments and play a pivotal role in the selenium cycle. Unlike its structural analogues oxygen and sulfur, the chalcogen selenium and its microbial cycling have received much less attention by the scientific community. This review focuses on microorganisms that use selenate and selenite as terminal electron acceptors, in parallel to the well-studied sulfate-reducing bacteria. It overviews the significant advancements made in recent years on the role of SeRB in the biological selenium cycle and their ecological role, phylogenetic characterization, and metabolism, as well as selenium biomineralization mechanisms and environmental biotechnological applications. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

New insights into the role of phosphate-free lipids in anaerobic environments

NASA Astrophysics Data System (ADS)

Schubotz, F.; De Santiago Torio, A.; Kuehl, J.; Grant, C.; Rahn-Lee, L.; Arkin, A. P.; Deutschbauer, A. M.; Summons, R. E.; Bosak, T.

2016-02-01

Recent investigations have revealed an abundance of phosphate-free glycolipids and aminolipids, classically assigned to oxygenic phototrophs, in anoxic environments where anaerobic microorganisms prevail. Phosphorus-free lipids in oxic environments are thought to indicate an adaptation to phosphorus limitation, but their significance in anoxic environments is unclear, because these environments are not typically thought of as phosphorus-limited. We hypothesize that glycolipids and aminolipids play an overlooked and potentially integral role in anaerobic bacteria from marine and terrestrial environments and test this hypothesis in environmentally relevant model anaerobic deltaproteobacteria. None of the investigated strains of the sulfate-reducing genus Desulfovibrio synthesize glycolipids under normal growth conditions or during nitrogen limitation. However, when growing in phosphate-limited conditions, all investigated organisms undergo a nearly complete replacement of phospholipids by glycolipids. Some phosphate-starved organisms, such as D. fructosivorans, are also able to synthesize betaine lipids. Analyses of mutants of Desulfovibrio alaskensis G20 identify genes responsible for the biosynthesis of aminolipids (Dde_3661) and glycolipids (Dde_3613). Fitness experiments using tagged transposon mutant libraries of G20 identify these two genes and 90 other genes important for fitness of this organism during phosphate limitation. These experiments identify for the first time betaine lipids and glycolipids in sulfate-reducing bacteria and demonstrate the importance of these non-phosphorus lipids as substitute lipids in obligate anaerobes. These findings suggest that phosphorus availability limits microbial growth and activity in a more widespread range of environments than previously thought.

The Leucine Incorporation Method Estimates Bacterial Growth Equally Well in Both Oxic and Anoxic Lake Waters

PubMed Central

Bastviken, David; Tranvik, Lars

2001-01-01

Bacterial biomass production is often estimated from incorporation of radioactively labeled leucine into protein, in both oxic and anoxic waters and sediments. However, the validity of the method in anoxic environments has so far not been tested. We compared the leucine incorporation of bacterial assemblages growing in oxic and anoxic waters from three lakes differing in nutrient and humic contents. The method was modified to avoid O2 contamination by performing the incubation in syringes. Isotope saturation levels in oxic and anoxic waters were determined, and leucine incorporation rates were compared to microscopically observed bacterial growth. Finally, we evaluated the effects of O2 contamination during incubation with leucine, as well as the potential effects of a headspace in the incubation vessel. Isotope saturation occurred at a leucine concentration of above about 50 nM in both oxic and anoxic waters from all three lakes. Leucine incorporation rates were linearly correlated to observed growth, and there was no significant difference between oxic and anoxic conditions. O2 contamination of anoxic water during 1-h incubations with leucine had no detectable impact on the incorporation rate, while a headspace in the incubation vessel caused leucine incorporation to increase in both anoxic and O2-contaminated samples. The results indicate that the leucine incorporation method relates equally to bacterial growth rates under oxic and anoxic conditions and that incubation should be performed without a headspace. PMID:11425702

Microbial community of a hydrothermal mud vent underneath the deep-sea anoxic brine lake Urania (eastern Mediterranean).

PubMed

Yakimov, Michail M; Giuliano, Laura; Cappello, Simone; Denaro, Renata; Golyshin, Peter N

2007-04-01

The composition of a metabolically active prokaryotic community thriving in hydrothermal mud fluids of the deep-sea hypersaline anoxic Western Urania Basin was characterized using rRNA-based phylogenetic analysis of a clone library. The physiologically active prokaryotic assemblage in this extreme environment showed a great genetic diversity. Most members of the microbial community appeared to be affiliated to yet uncultured organisms from similar ecosystems, i.e., deep-sea hypersaline basins and hydrothermal vents. The bacterial clone library was dominated by phylotypes affiliated with the epsilon-Proteobacteria subdivision recognized as an ecologically significant group of bacteria inhabiting deep-sea hydrothermal environments. Almost 18% of all bacterial clones were related to delta-Proteobacteria, suggesting that sulfate reduction is one of the dominant metabolic processes occurring in warm mud fluids. The remaining bacterial phylotypes were related to alpha- and beta-Proteobacteria, Actinobacteria, Bacteroides, Deinococcus-Thermus, KB1 and OP-11 candidate divisions. Moreover, a novel monophyletic clade, deeply branched with unaffiliated 16S rDNA clones was also retrieved from deep-sea sediments and halocline of Urania Basin. Archaeal diversity was much lower and detected phylotypes included organisms affiliated exclusively with the Euryarchaeota. More than 96% of the archaeal clones belonged to the MSBL-1 candidate order recently found in hypersaline anoxic environments, such as endoevaporitic microbial mats, Mediterranean deep-sea mud volcanoes and anoxic basins. Two phylotypes, represented by single clones were related to uncultured groups DHVE-1 and ANME-1. Thus, the hydrothermal mud of hypersaline Urania Basin seems to contain new microbial diversity. The prokaryotic community was significantly different from that occurring in the upper layers of the Urania Basin since 60% of all bacterial and 40% of all archaeal phylotypes were obtained only from mud

Presence of Pathogenic Bacteria and Viruses in the Daycare Environment.

PubMed

Ibfelt, Tobias; Engelund, Eva Hoy; Permin, Anders; Madsen, Jonas Stenløkke; Schultz, Anna Charlotte; Andersen, Leif Percival

2015-10-01

The number of children in daycare centers (DCCs) is rising. This increases exposure to microorganisms and infectious diseases. Little is known about which bacteria and viruses are present in the DCC environment and where they are located. In the study described in this article, the authors set out to determine the prevalence of pathogenic bacteria and viruses and to find the most contaminated fomites in DCCs. Fifteen locations in each DCC were sampled for bacteria, respiratory viruses, and gastrointestinal viruses. The locations were in the toilet, kitchen, and playroom areas and included nursery pillows, toys, and tables, among other things. Coliform bacteria were primarily found in the toilet and kitchen areas whereas nasopharyngeal bacteria were found mostly on toys and fabric surfaces in the playroom. Respiratory viruses were omnipresent in the DCC environment, especially on the toys.

Manganese Driven Carbon Oxidation along Oxic-Anoxic Interfaces in Forest Soils

NASA Astrophysics Data System (ADS)

Jones, M. E.; Keiluweit, M.

2017-12-01

Soils are the largest and most dynamic terrestrial carbon pool, storing a total of 3000 Pg of C - more than the atmosphere and biosphere combined. Because microbial oxidation determines the proportion of carbon that is either stored in the soil or emitted as climate active CO2, its rate directly impacts the global carbon cycle. Recently, a strong correlation between oxidation rates and manganese (Mn) content has been observed in forest soils globally, leading researchers conclude that Mn "is the single main factor governing" the oxidation of plant-derived particulate organic carbon (POC). Many soils are characterized by steep oxygen gradients, forming oxic-anoxic transitions that enable rapid redox cycling of Mn. Oxic-anoxic interfaces have been shown to promote fungal Mn oxidation and the formation of ligand-stabilized Mn(III), which ranks second only to superoxide as the most powerful oxidizing agent in the environment. Here we examined fungal Mn(III) formation along redox gradients in forest soils and their impact on POC oxidation rates. In both field and laboratory settings, oxic-anoxic transition zones showed the greatest Mn(III) concentrations, along with enhanced fungal growth, oxidative potential, production of soluble oxidation products, and CO2 production. Additional electrochemical and X-ray (micro)spectroscopic analyses indicated that oxic-anoxic interfaces represent ideal niches for fungal Mn(III) formation, owing to the ready supply of Mn(II), ligands and O2. Combined, our results suggest that POC oxidation relies on fungal Mn cycling across oxic-anoxic interfaces to produce Mn(III) based oxidants. Because predicted changes in the frequency and timing of precipitation dramatically alter soil moisture regimes in forest soils, understanding the mechanistic link between Mn cycling and carbon oxidation along oxic-anoxic interfaces is becoming increasingly important.

Corrosion of Iron by Sulfate-Reducing Bacteria: New Views of an Old Problem

PubMed Central

Garrelfs, Julia

2014-01-01

About a century ago, researchers first recognized a connection between the activity of environmental microorganisms and cases of anaerobic iron corrosion. Since then, such microbially influenced corrosion (MIC) has gained prominence and its technical and economic implications are now widely recognized. Under anoxic conditions (e.g., in oil and gas pipelines), sulfate-reducing bacteria (SRB) are commonly considered the main culprits of MIC. This perception largely stems from three recurrent observations. First, anoxic sulfate-rich environments (e.g., anoxic seawater) are particularly corrosive. Second, SRB and their characteristic corrosion product iron sulfide are ubiquitously associated with anaerobic corrosion damage, and third, no other physiological group produces comparably severe corrosion damage in laboratory-grown pure cultures. However, there remain many open questions as to the underlying mechanisms and their relative contributions to corrosion. On the one hand, SRB damage iron constructions indirectly through a corrosive chemical agent, hydrogen sulfide, formed by the organisms as a dissimilatory product from sulfate reduction with organic compounds or hydrogen (“chemical microbially influenced corrosion”; CMIC). On the other hand, certain SRB can also attack iron via withdrawal of electrons (“electrical microbially influenced corrosion”; EMIC), viz., directly by metabolic coupling. Corrosion of iron by SRB is typically associated with the formation of iron sulfides (FeS) which, paradoxically, may reduce corrosion in some cases while they increase it in others. This brief review traces the historical twists in the perception of SRB-induced corrosion, considering the presently most plausible explanations as well as possible early misconceptions in the understanding of severe corrosion in anoxic, sulfate-rich environments. PMID:24317078

Post-anoxic denitrification via nitrite driven by PHB in feast-famine sequencing batch reactor.

PubMed

Chen, Hong-Bo; Yang, Qi; Li, Xiao-Ming; Wang, Yan; Luo, Kun; Zeng, Guang-Ming

2013-08-01

Recently, it was found that excess phosphorus removal could be induced by aerobic/extended-idle regime. In this study, an anoxic period was introduced after the aeration to realize simultaneous nitrogen and phosphorus removal. The results demonstrated that stable partial nitrification could be achieved by controlling the aeration duration at 2.5h because it could not only obtain a desirable ammonia oxidation to nitrite but also avoid the extensive aeration converting nitrite to nitrate, and moreover, the accumulated poly-3-hydroxybutyrate still remain in a relative sufficient concentration (1.5mmolCg(-1) VSS), which could subsequently served as internal carbon source for post-anoxic denitrification. The nitrite accumulation ratio was observed to have relatively high correlation with biological nutrient removal. Over stages with stable high-level nitrite accumulation, the process achieved desirable and stable nitrogen and phosphorus removal efficiencies averaging 95% and 99% respectively. Fluorescence in situ hybridization analysis showed that the faster growth rate of the ammonia oxidizing bacteria than the nitrite oxidizing bacteria was the main reason for achieving nitrite accumulation. In addition, the secondary phosphorus release was negligible and the process maintained excellent nutrient removal under low influent ammonia nitrogen. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bacterial ethane formation from reduced, ethylated sulfur compounds in anoxic sediments

USGS Publications Warehouse

Oremland, R.S.; Whiticar, Michael J.; Strohmaier, F.E.; Kiene, R.P.

1988-01-01

Trace levels of ethane were produced biologically in anoxic sediment slurries from five chemically different aquatic environments. Gases from these locations displayed biogenic characteristics, having 12C-enriched values of ??13CH4 (-62 to -86%.), ??13C2H6 (-35 to -55%.) and high ratios (720 to 140,000) of CH4 [C2H6 + C3H8]. Endogenous production of ethane by slurries was inhibited by autoclaving or by addition of the inhibitor of methanogenic bacteria, 2-bromoethanesulfonic acid (BES). Ethane formation was stimulated markedly by ethanethiol (ESH), and, to a lesser extent, by diethylsulfide (DES). Formation of methane and ethane in ESH- or DES-amended slurries was blocked by BES. Experiments showed that ethionine (or an analogous compound) could be a precursor of ESH. Ethylamine or ethanol additions to slurries caused only a minor stimulation of ethane formation. Similarly, propanethiol additions resulted in only a minor enhancement of propane formation. Cell suspensions of a methyltrophic methanogen produced traces of ethane when incubated in the presence of DES, although the organism did not grow on this compound. These results indicate that methanogenic bacteria produce ethane from the traces of ethylated sulfur compounds present in recent sediments. Preliminary estimates of stable carbon isotope fractionation associated with sediment methane formation from dimethylsulfide was about 40%., while ethane formation from DES and ESH was only 4. 6 and 6.5%., respectively. ?? 1988.

Transmission of Airborne Bacteria across Built Environments and Its Measurement Standards: A Review.

PubMed

Fujiyoshi, So; Tanaka, Daisuke; Maruyama, Fumito

2017-01-01

Human health is influenced by various factors including microorganisms present in built environments where people spend most of their lives (approximately 90%). It is therefore necessary to monitor and control indoor airborne microbes for occupational safety and public health. Most studies concerning airborne microorganisms have focused on fungi, with scant data available concerning bacteria. The present review considers papers published from 2010 to 2017 approximately and factors affecting properties of indoor airborne bacteria (communities and concentration) with respect to temporal perspective and to multiscale interaction viewpoint. From a temporal perspective, bacterial concentrations in built environments change depending on numbers of human occupancy, while properties of bacterial communities tend to remain stable. Similarly, the bacteria found in social and community spaces such as offices, classrooms and hospitals are mainly associated with human occupancy. Other major sources of indoor airborne bacteria are (i) outdoor environments, and (ii) the building materials themselves. Indoor bacterial communities and concentrations are varied with varying interferences by outdoor environment. Airborne bacteria from the outdoor environment enter an indoor space through open doors and windows, while indoor bacteria are simultaneously released to the outer environment. Outdoor bacterial communities and their concentrations are also affected by geographical factors such as types of land use and their spatial distribution. The bacteria found in built environments therefore originate from any of the natural and man-made surroundings around humans. Therefore, to better understand the factors influencing bacterial concentrations and communities in built environments, we should study all the environments that humans contact as a single ecosystem. In this review, we propose the establishment of a standard procedure for assessing properties of indoor airborne bacteria using

Transmission of Airborne Bacteria across Built Environments and Its Measurement Standards: A Review

PubMed Central

Fujiyoshi, So; Tanaka, Daisuke; Maruyama, Fumito

2017-01-01

Human health is influenced by various factors including microorganisms present in built environments where people spend most of their lives (approximately 90%). It is therefore necessary to monitor and control indoor airborne microbes for occupational safety and public health. Most studies concerning airborne microorganisms have focused on fungi, with scant data available concerning bacteria. The present review considers papers published from 2010 to 2017 approximately and factors affecting properties of indoor airborne bacteria (communities and concentration) with respect to temporal perspective and to multiscale interaction viewpoint. From a temporal perspective, bacterial concentrations in built environments change depending on numbers of human occupancy, while properties of bacterial communities tend to remain stable. Similarly, the bacteria found in social and community spaces such as offices, classrooms and hospitals are mainly associated with human occupancy. Other major sources of indoor airborne bacteria are (i) outdoor environments, and (ii) the building materials themselves. Indoor bacterial communities and concentrations are varied with varying interferences by outdoor environment. Airborne bacteria from the outdoor environment enter an indoor space through open doors and windows, while indoor bacteria are simultaneously released to the outer environment. Outdoor bacterial communities and their concentrations are also affected by geographical factors such as types of land use and their spatial distribution. The bacteria found in built environments therefore originate from any of the natural and man-made surroundings around humans. Therefore, to better understand the factors influencing bacterial concentrations and communities in built environments, we should study all the environments that humans contact as a single ecosystem. In this review, we propose the establishment of a standard procedure for assessing properties of indoor airborne bacteria using

Phthalates biodegradation in the environment.

PubMed

Liang, Da-Wei; Zhang, Tong; Fang, Herbert H P; He, Jianzhong

2008-08-01

Phthalates are synthesized in massive amounts to produce various plastics and have become widespread in environments following their release as a result of extensive usage and production. This has been of an environmental concern because phthalates are hepatotoxic, teratogenic, and carcinogenic by nature. Numerous studies indicated that phthalates can be degraded by bacteria and fungi under aerobic, anoxic, and anaerobic conditions. This paper gives a review on the biodegradation of phthalates and includes the following aspects: (1) the relationship between the chemical structure of phthalates and their biodegradability, (2) the biodegradation of phthalates by pure/mixed cultures, (3) the biodegradation of phthalates under various environments, and (4) the biodegradation pathways of phthalates.

Adhesion of Biodegradative Anaerobic Bacteria to Solid Surfaces

PubMed Central

van Schie, Paula M.; Fletcher, Madilyn

1999-01-01

In order to exploit the ability of anaerobic bacteria to degrade certain contaminants for bioremediation of polluted subsurface environments, we need to understand the mechanisms by which such bacteria partition between aqueous and solid phases, as well as the environmental conditions that influence partitioning. We studied four strictly anaerobic bacteria, Desulfomonile tiedjei, Syntrophomonas wolfei, Syntrophobacter wolinii, and Desulfovibrio sp. strain G11, which theoretically together can constitute a tetrachloroethylene- and trichloroethylene-dechlorinating consortium. Adhesion of these organisms was evaluated by microscopic determination of the numbers of cells that attached to glass coverslips exposed to cell suspensions under anaerobic conditions. We studied the effects of the growth phase of the organisms on adhesion, as well as the influence of electrostatic and hydrophobic properties of the substratum. Results indicate that S. wolfei adheres in considerably higher numbers to glass surfaces than the other three organisms. Starvation greatly decreases adhesion of S. wolfei and Desulfovibrio sp. strain G11 but seems to have less of an effect on the adhesion of the other bacteria. The presence of Fe3+ on the substratum, which would be electropositive, significantly increased the adhesion of S. wolfei, whereas the presence of silicon hydrophobic groups decreased the numbers of attached cells of all species. Measurements of transport of cells through hydrophobic-interaction and electrostatic-interaction columns indicated that all four species had negatively charged cell surfaces and that D. tiedjei and Desulfovibrio sp. strain G11 possessed some hydrophobic cell surface properties. These findings are an early step toward understanding the dynamic attachment of anaerobic bacteria in anoxic environments. PMID:10543826

Spatio-temporal dynamics of sulfate-reducing bacteria in extreme environment of Rogoznica Lake revealed by 16S rRNA analysis

NASA Astrophysics Data System (ADS)

Čanković, Milan; Petrić, Ines; Marguš, Marija; Ciglenečki, Irena

2017-08-01

Highly eutrophic and euxinic seawater system of Rogoznica Lake (Croatia) was used as a study site for investigation of distribution, diversity and abundance of sulfate-reducing bacteria (SRB) during stratified conditions in the summer and winter season, by targeting 6 phylogenetic subgroups of SRB. 16S rRNA gene sequences indicated that community cannot be directly related to cultured SRB species but rather that Rogoznica Lake harbors habitat-specific SRB populations associated to bacteria belonging to δ-Proteobacteria with few Firmicutes and Verrucomicrobium-related populations. Clear spatial-temporal shifts in the SRB community structure were observed. Results implied existence of distinct SRB populations between the water column and sediment, as well as higher diversity of the SRB occupying water layer then the ones found in the sediment. Likewise, seasonal variations in populations were observed. While SRB community was more diverse in the winter compared to the summer season in the water layer, situation was opposite in the sediment. Water layer communities seem to be more susceptible to changes of physico-chemical parameters, while those in the sediment have prorogated response to these changes. Results indicate that SRB diversity is still highly underestimated in natural environments, especially in specific habitats such as Rogoznica Lake. Presented data show a complex SRB diversity and distribution supporting the idea that habitat-specific SRB communities are important part of the anaerobic food chain in degradation of organic matter as well as cycling of sulfur and carbon species in the Lake and similar anoxic environment.

Microbial oceanography of anoxic oxygen minimum zones.

PubMed

Ulloa, Osvaldo; Canfield, Donald E; DeLong, Edward F; Letelier, Ricardo M; Stewart, Frank J

2012-10-02

Vast expanses of oxygen-deficient and nitrite-rich water define the major oxygen minimum zones (OMZs) of the global ocean. They support diverse microbial communities that influence the nitrogen economy of the oceans, contributing to major losses of fixed nitrogen as dinitrogen (N(2)) and nitrous oxide (N(2)O) gases. Anaerobic microbial processes, including the two pathways of N(2) production, denitrification and anaerobic ammonium oxidation, are oxygen-sensitive, with some occurring only under strictly anoxic conditions. The detection limit of the usual method (Winkler titrations) for measuring dissolved oxygen in seawater, however, is much too high to distinguish low oxygen conditions from true anoxia. However, new analytical technologies are revealing vanishingly low oxygen concentrations in nitrite-rich OMZs, indicating that these OMZs are essentially anoxic marine zones (AMZs). Autonomous monitoring platforms also reveal previously unrecognized episodic intrusions of oxygen into the AMZ core, which could periodically support aerobic metabolisms in a typically anoxic environment. Although nitrogen cycling is considered to dominate the microbial ecology and biogeochemistry of AMZs, recent environmental genomics and geochemical studies show the presence of other relevant processes, particularly those associated with the sulfur and carbon cycles. AMZs correspond to an intermediate state between two "end points" represented by fully oxic systems and fully sulfidic systems. Modern and ancient AMZs and sulfidic basins are chemically and functionally related. Global change is affecting the magnitude of biogeochemical fluxes and ocean chemical inventories, leading to shifts in AMZ chemistry and biology that are likely to continue well into the future.

Microbial oceanography of anoxic oxygen minimum zones

PubMed Central

Ulloa, Osvaldo; Canfield, Donald E.; DeLong, Edward F.; Letelier, Ricardo M.; Stewart, Frank J.

2012-01-01

Vast expanses of oxygen-deficient and nitrite-rich water define the major oxygen minimum zones (OMZs) of the global ocean. They support diverse microbial communities that influence the nitrogen economy of the oceans, contributing to major losses of fixed nitrogen as dinitrogen (N2) and nitrous oxide (N2O) gases. Anaerobic microbial processes, including the two pathways of N2 production, denitrification and anaerobic ammonium oxidation, are oxygen-sensitive, with some occurring only under strictly anoxic conditions. The detection limit of the usual method (Winkler titrations) for measuring dissolved oxygen in seawater, however, is much too high to distinguish low oxygen conditions from true anoxia. However, new analytical technologies are revealing vanishingly low oxygen concentrations in nitrite-rich OMZs, indicating that these OMZs are essentially anoxic marine zones (AMZs). Autonomous monitoring platforms also reveal previously unrecognized episodic intrusions of oxygen into the AMZ core, which could periodically support aerobic metabolisms in a typically anoxic environment. Although nitrogen cycling is considered to dominate the microbial ecology and biogeochemistry of AMZs, recent environmental genomics and geochemical studies show the presence of other relevant processes, particularly those associated with the sulfur and carbon cycles. AMZs correspond to an intermediate state between two “end points” represented by fully oxic systems and fully sulfidic systems. Modern and ancient AMZs and sulfidic basins are chemically and functionally related. Global change is affecting the magnitude of biogeochemical fluxes and ocean chemical inventories, leading to shifts in AMZ chemistry and biology that are likely to continue well into the future. PMID:22967509

On the Occurrence of Anoxic Microniches, Denitrification, and Sulfate Reduction in Aerated Activated Sludge

PubMed Central

Schramm, Andreas; Santegoeds, Cecilia M.; Nielsen, Helle K.; Ploug, Helle; Wagner, Michael; Pribyl, Milan; Wanner, Jiri; Amann, Rudolf; de Beer, Dirk

1999-01-01

A combination of different methods was applied to investigate the occurrence of anaerobic processes in aerated activated sludge. Microsensor measurements (O2, NO2−, NO3−, and H2S) were performed on single sludge flocs to detect anoxic niches, nitrate reduction, or sulfate reduction on a microscale. Incubations of activated sludge with 15NO3− and 35SO42− were used to determine denitrification and sulfate reduction rates on a batch scale. In four of six investigated sludges, no anoxic zones developed during aeration, and consequently denitrification rates were very low. However, in two sludges anoxia in flocs coincided with significant denitrification rates. Sulfate reduction could not be detected in any sludge in either the microsensor or the batch investigation, not even under short-term anoxic conditions. In contrast, the presence of sulfate-reducing bacteria was shown by fluorescence in situ hybridization with 16S rRNA-targeted oligonucleotide probes and by PCR-based detection of genes coding for the dissimilatory sulfite reductase. A possible explanation for the absence of anoxia even in most of the larger flocs might be that oxygen transport is not only diffusional but enhanced by advection, i.e., facilitated by flow through pores and channels. This possibility is suggested by the irregularity of some oxygen profiles and by confocal laser scanning microscopy of the three-dimensional floc structures, which showed that flocs from the two sludges in which anoxic zones were found were apparently denser than flocs from the other sludges. PMID:10473433

Anoxic control of odour and corrosion from sewer networks.

PubMed

Yang, W; Vollertsen, J; Hvitved-Jacobsen, T

2004-01-01

Anoxic processes can effectively control odour and corrosion in sewer networks. However, the absence of fundamental knowledge on the kinetics of anoxic transformation of sewage prevents the engineering applications of anoxic control in sewers. This paper focuss on a basic understanding of the anoxic transformations needed for a conceptual simulation of the water phase processes. Experiments conducted in batch reactors have shown that nitrite builds up in wastewater during denitrification. Part of the nitrate-reducing biomass is capable of utilizing nitrite after nitrate is depleted. Compared with aerobic transformation, anoxic processes have low values of maximum growth rate of the biomass and also a low endogenous respiration rate. Heterotrophic yield determined under anoxic conditions, at level of 0.25 mmol e-eq (mmol e-eq)(-1), accounted for less than 40% of the corresponding aerobic values.

The Cenomanian-Turonian oceanic anoxic event in Tibet, a real anoxic condition? Clues from Phosphorus, Carbon and Traces Elements accumulations.

NASA Astrophysics Data System (ADS)

Bomou, B.; Adatte, T.; Föllmi, K. B.; Caron, M.; Tantawy, A. A.; Fleitmann, D.; Matera, V.; Huang, Y.

2009-04-01

The Cenomanian-Turonian boundary is marked by an Oceanic Anoxic Event (OAE 2) characterized by finely laminated organic carbon rich sediments deposited under oxygen depleted conditions, coinciding with a positive shift in δ13C isotope excursion. The main goal of the present research is to get a better understanding of mechanisms which triggered these OAEs, and particularly the paleoenvironmental conditions which characterized the onset of that major anoxic event and their evolution. Mort (2007) demonstrated that the onset of the Cenomanian-Turonian OAE was triggered by a short-lived but significant increase in phosphorus burial. Then bottom waters became anoxic and switched from being a P sink to a P source, sustaining the productivity in a positive feedback loop. Increased aridity, removal of atmospheric CO2 by burial as organic carbon in black shales and reduction in nutrient availability may have been factors bringing about the return to more oxic oceans. However, Total Phosphorus (Ptot) and trace metals behaviour is not well known at larger scale, away from main black shales source (Western Tethys and Central Atlantic). It is especially interesting to see if P distribution will show a similar maximum predating the positive carbon excursion. We investigate therefore the section of Gongzha (Tibet, China) located at the north margin of the Indian plate in the Tethys Himalayas zone (SE Tethys). These sediments are deposited in open marine basin and slope settings under hemipelagic environment (Li et al., 2006). Clay analyses show that the sediments have been overprinted by burial diagenesis and tectonic processes, but the biostratigraphy by foraminifera and nannofossils, microfacies and carbon stable isotopes data indicate a quite good preservation and absence of significant hiatus. Carbon isotope analyses exhibit the classical C-T positive shift with a first peak near the end of R. cushmani zone, a second in the lower part of W. archaeocretacea zone, followed by

Bio-desulfurization and denitrification by anaerobic-anoxic process for the treatment of wastewater from flue gas washing.

PubMed

Song, Ziyu; Zhou, Xuemei; Li, Yuguang; Yang, Maohua; Xing, Jianmin

2013-01-01

For amine-based carbon dioxide capture, nitrogen oxides and sulfur oxides were the main pollutants that had a negative effect on the regeneration of solvent. Before carbon dioxide capture, the sulfur oxides in flue gas should be removed by the method of calcium salt, and then washed by alkaline solution to eliminate the residual nitrogen oxides and sulfur oxides. The washing wastewater containing sulfate and nitrate needs to be treated. In this study, a novel anaerobic-anoxic process was built up for the treatment of this washing wastewater. Nitrate was reduced to nitrogen by denitrifying bacteria. Sulfate was firstly reduced to sulfide by sulfate reducing bacteria, and then selectively oxidized to element sulfur by sulfide oxidizing bacteria. The treated liquid could be reused as absorption after the adjustment of pH value. The performances of this bioprocess were investigated under various pH values and S/N ratios. It was found that the optimal pH value of influent was 6.0, the percentages of denitrification and sulfate reducing could reach 90 and 89%, respectively. Seventy-six percent of sulfate was transformed into element sulfur. Nitrate significantly had a negative effect on sulfate reduction above 10 mM. As 20 mM nitrate, the sulfate reducing percentage would drop to 67%. These results showed that the anaerobic-anoxic process was feasible for the treatment of flue gas washing wastewater. It would be prospectively applied to other wastewater with the higher ratio of SO4(2-)/NO3(-).

Uranium(IV) adsorption by natural organic matter in anoxic sediments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bone, Sharon E.; Dynes, James J.; Cliff, John

2017-01-09

Uranium is an important fuel source and a global environmental contaminant. It accumulates in the tetravalent state, U(IV), in anoxic sediments, including ore deposits, marine basins, and contaminated aquifers. However, very little is known about the speciation of U(IV) in low temperature geochemical environments, inhibiting the development of a conceptual model of U behavior. Until recently, U(IV) was assumed to exist predominantly as the sparingly soluble mineral uraninite (UO 2) in anoxic sediments; yet studies now show that UO 2 is not often dominant in these environments. However, a model of U(IV) speciation under environmentally relevant conditions has not yetmore » been developed. Here we show that complexes of U(IV) adsorb on organic carbon and organic carbon-coated clays in an organic-rich natural substrate under field-relevant conditions. Whereas previous research assumed that the U(IV) product depended on the reduction pathway, our results demonstrate that UO 2 formation can be inhibited simply by decreasing the U:solid ratio. Thus, it is the number and type of surface ligands that controls U(IV) speciation subsequent to U(VI) reduction. Projections of U transport and bioavailability, and thus its threat to human and ecosystem health, must consider retention of U(IV) ions within the local sediment environment.« less

Effects of glucose on microcystin-LR removal and the bacterial community composition through anoxic biodegradation in drinking water sludge.

PubMed

Ma, Guangxiang; Pei, Haiyan; Hu, Wenrong; Xu, Xiangchao; Ma, Chunxia; Pei, Ruoting

2016-01-01

To enhance the degradation efficiency of microcystin (MC) in drinking water sludge (DWS), the underlying mechanisms between organic carbon (glucose) and the biodegradation of MC-LR under anoxic conditions were investigated by polymerase chain reaction-denaturing gradient gel electrophoresis technology. The addition of glucose reduced the rate of the MC-LR biodegradation indicating the occurrence of inhibition of degradation, and an increased inhibition was observed with increases in glucose concentration (0-10,000 mg/L). In addition, the community analysis indicated that the variety and the number of the microbes increased with the concentration of glucose amended (0 -1000 mg/L), but they decreased substantially with the addition of 10,000 mg/L of glucose. The phyla Firmicutes, Proteobacteria and Chloroflexi were found to be the dominant. Methylobacterium and Sphingomonas were MC-degrading bacteria and used glucose as a prior carbon source instead of MC, resulting in the decrease in the MC-LR biodegradation rate under anoxic conditions. Thus, reducing organic carbon could improve the anoxic biodegradation efficiency of MC in DWS.

Phylogenetic diversity of archaea and bacteria in the anoxic zone of a meromictic lake (Lake Pavin, France).

PubMed

Lehours, Anne-Catherine; Evans, Paul; Bardot, Corinne; Joblin, Keith; Gérard, Fonty

2007-03-01

The compositions of archaeal and bacterial populations at different depths (60 m [mixolimnion-chemocline interface], 70 m [chemocline-subchemocline interface], 90 m, and 92 m [the water-sediment interface]) in the anoxic zone of the water column in Lake Pavin, a freshwater permanently stratified mountain lake in France, were determined. Phylogenetic trees were constructed from sequences to assess archaeal and bacterial diversity at the four sites.

Energetics and Application of Heterotrophy in Acetogenic Bacteria

PubMed Central

Schuchmann, Kai

2016-01-01

Acetogenic bacteria are a diverse group of strictly anaerobic bacteria that utilize the Wood-Ljungdahl pathway for CO2 fixation and energy conservation. These microorganisms play an important part in the global carbon cycle and are a key component of the anaerobic food web. Their most prominent metabolic feature is autotrophic growth with molecular hydrogen and carbon dioxide as the substrates. However, most members also show an outstanding metabolic flexibility for utilizing a vast variety of different substrates. In contrast to autotrophic growth, which is hardly competitive, metabolic flexibility is seen as a key ability of acetogens to compete in ecosystems and might explain the almost-ubiquitous distribution of acetogenic bacteria in anoxic environments. This review covers the latest findings with respect to the heterotrophic metabolism of acetogenic bacteria, including utilization of carbohydrates, lactate, and different alcohols, especially in the model acetogen Acetobacterium woodii. Modularity of metabolism, a key concept of pathway design in synthetic biology, together with electron bifurcation, to overcome energetic barriers, appears to be the basis for the amazing substrate spectrum. At the same time, acetogens depend on only a relatively small number of enzymes to expand the substrate spectrum. We will discuss the energetic advantages of coupling CO2 reduction to fermentations that exploit otherwise-inaccessible substrates and the ecological advantages, as well as the biotechnological applications of the heterotrophic metabolism of acetogens. PMID:27208103

Modeling anoxic aggregates in the ocean - implications for nitrogen, sulfur and trace metal cycling

NASA Astrophysics Data System (ADS)

Bianchi, D.; Weber, T. S.; Deutsch, C.

2016-02-01

Anoxic conditions are uncommon in the open ocean, and mostly confined to the cores of oxygen minimum zones (OMZs). When oxygen runs out, a suite of alternative electron acceptors are used, leading to denitrification and, rarely in open waters, sulfate reduction. Anoxic conditions have been shown to develop inside millimeter-scale organic particles and aggregates, establishing microscale gradients that could sustain diverse microbial communities along a sequence of redox niches. We develop a model of the biogeochemistry of anoxic aggregates that includes aerobic and anaerobic reactions in a diffusion-limited environment, and present analytical and numerical solutions for the conditions that allow denitrification and sulfate reduction inside aggregates. The model is applied to realistic size spectra of particles sinking through the water column, and used to estimate the potential for particle-bound denitrification and sulfate reduction in the global ocean. We show that anoxia inside aggregates may be common throughout low oxygen waters, extending the niche of denitrifying metabolisms beyond fully anoxic zones. In the OMZ cores, aggregates can sustain pockets of sulfate reduction in otherwise non-sulfidic waters, depending on ambient nitrate concentrations, particle respiration rates, and other factors. We further discuss the implications for nitrogen, sulfur and trace metal cycling in the ocean.

Metabolism in anoxic permeable sediments is dominated by eukaryotic dark fermentation

NASA Astrophysics Data System (ADS)

Bourke, Michael F.; Marriott, Philip J.; Glud, Ronnie N.; Hasler-Sheetal, Harald; Kamalanathan, Manoj; Beardall, John; Greening, Chris; Cook, Perran L. M.

2017-01-01

Permeable sediments are common across continental shelves and are critical contributors to marine biogeochemical cycling. Organic matter in permeable sediments is dominated by microalgae, which as eukaryotes have different anaerobic metabolic pathways to bacteria and archaea. Here we present analyses of flow-through reactor experiments showing that dissolved inorganic carbon is produced predominantly as a result of anaerobic eukaryotic metabolic activity. In our experiments, anaerobic production of dissolved inorganic carbon was consistently accompanied by large dissolved H2 production rates, suggesting the presence of fermentation. The production of both dissolved inorganic carbon and H2 persisted following administration of broad spectrum bactericidal antibiotics, but ceased following treatment with metronidazole. Metronidazole inhibits the ferredoxin/hydrogenase pathway of fermentative eukaryotic H2 production, suggesting that pathway as the source of H2 and dissolved inorganic carbon production. Metabolomic analysis showed large increases in lipid production at the onset of anoxia, consistent with documented pathways of anoxic dark fermentation in microalgae. Cell counts revealed a predominance of microalgae in the sediments. H2 production was observed in dark anoxic cultures of diatoms (Fragilariopsis sp.) and a chlorophyte (Pyramimonas) isolated from the study site, substantiating the hypothesis that microalgae undertake fermentation. We conclude that microalgal dark fermentation could be an important energy-conserving pathway in permeable sediments.

Assessment of airborne bacteria in selected occupational environments in Quezon City, Philippines.

PubMed

Rendon, Rhoshela Vi C; Garcia, Bea Clarise B; Vital, Pierangeli G

2017-05-04

Exposure to bioaerosols has been associated with health deterioration among workers in several occupational environments. This highlights the need to study the microbiological quality of air of workplaces as no such study has been conducted yet in the Philippines. To detect and characterize the culturable mesophilic airborne bacteria in selected occupational environments we used passive sedimentation technique. It was observed that the number of colony-forming units was highest in junk shop, followed by the light railway transit station and last the office. By contrast, the bacterial composition was similar in all sites: Gram-positive cocci > Gram-positive bacilli > Gram-negative bacteria. Staphylococcus aureus and Bacillus spp. were also detected in all sites. These findings suggest that the presence of airborne bacteria may be a potential health hazard in urban occupational environments in the Philippines.

Ecologically and Geologically Relevant Isotope Signatures of C, N, and S in Okenone Producing Purple Sulfur Bacteria

NASA Astrophysics Data System (ADS)

Smith, D.; Steele, A.; Bowden, R.; Fogel, M. L.

2013-12-01

The carbon (C), nitrogen (N), and sulfur (S) cycles are linked in euxinic environments by purple sulfur bacteria (PSB). PSB could be responsible for the isotopic enrichments that have been observed in both fresh and marine anoxic basins. Okenane, the only recognized molecular fossil unique to PSB, is derived from okenone, a carotenoid pigment unique to Chromatiaceae. Since PSB have this exclusive molecular fossil and are fundamental components in the overall ecology of euxinic environments, a comprehensive study was undertaken to assess the C, N, and S metabolisms PSB carryout under precise laboratory conditions. The consequential isotopic fractionations that may be documented in modern environments and geologic record were examined. Autotrophic cultures of Marichromatium purpuratum DSMZ 1591 (Mpurp1591) were observed to have a fractionation between CO2 and biomass (Δ13Cbiomass - CO2), ranging from -16.1 to -37.6‰, dependent on growth stage. This rather large range of CO2 fractionation expands previously reported values for RuBisCO in PSB. Ammonium assimilation, controlled by glutamate dehydrogenase, was shown to have a fractionation (Δ15Nbiomass - NH4) of -15‰ in autotrophic cultures of Mpurp1591 and Thiocapsa marina 5653, documented for the first time in PSB. While it has been previously shown that phototrophic sulfur oxidizing bacteria connect sulfur and carbon cycling in euxinic ecosystems, the percentage of elemental sulfur and bulk biomass δ34S values of Mpurp1591 cells were contingent upon their carbon metabolisms. Here we show that the isotopic enrichments of S and N observed in freshwater and marine anoxic basins could be explained by the prevalence of PSB.

Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics

PubMed Central

Llorens-Marès, Tomàs; Yooseph, Shibu; Goll, Johannes; Hoffman, Jeff; Vila-Costa, Maria; Borrego, Carles M; Dupont, Chris L; Casamayor, Emilio O

2015-01-01

Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO2 fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems. PMID:25575307

Microbial responses to chitin and chitosan in oxic and anoxic agricultural soil slurries

NASA Astrophysics Data System (ADS)

Wieczorek, A. S.; Hetz, S. A.; Kolb, S.

2014-06-01

Microbial degradation of chitin in soil substantially contributes to carbon cycling in terrestrial ecosystems. Chitin is globally the second most abundant biopolymer after cellulose and can be deacetylated to chitosan or can be hydrolyzed to N,N'-diacetylchitobiose and oligomers of N-acetylglucosamine by aerobic and anaerobic microorganisms. Which pathway of chitin hydrolysis is preferred by soil microbial communities is unknown. Supplementation of chitin stimulated microbial activity under oxic and anoxic conditions in agricultural soil slurries, whereas chitosan had no effect. Thus, the soil microbial community likely was more adapted to chitin as a substrate. In addition, this finding suggested that direct hydrolysis of chitin was preferred to the pathway that starts with deacetylation. Chitin was apparently degraded by aerobic respiration, ammonification, and nitrification to carbon dioxide and nitrate under oxic conditions. When oxygen was absent, fermentation products (acetate, butyrate, propionate, hydrogen, and carbon dioxide) and ammonia were detected, suggesting that butyric and propionic acid fermentation, along with ammonification, were likely responsible for anaerobic chitin degradation. In total, 42 different chiA genotypes were detected of which twenty were novel at an amino acid sequence dissimilarity of less than 50%. Various chiA genotypes responded to chitin supplementation and affiliated with a novel deep-branching bacterial chiA genotype (anoxic conditions), genotypes of Beta- and Gammaproteobacteria (oxic and anoxic conditions), and Planctomycetes (oxic conditions). Thus, this study provides evidence that detected chitinolytic bacteria were catabolically diverse and occupied different ecological niches with regard to oxygen availability enabling chitin degradation under various redox conditions on community level.

Microbial responses to chitin and chitosan in oxic and anoxic agricultural soil slurries

NASA Astrophysics Data System (ADS)

Wieczorek, A. S.; Hetz, S. A.; Kolb, S.

2014-02-01

Chitin is the second most abundant biopolymer in terrestrial ecosystems and is subject to microbial degradation. Chitin can be deacetylated to chitosan or can be hydrolyzed to N,N'-diacetylchitobiose and oligomers of N-acetylglucosamine by aerobic and anaerobic microorganisms. Which pathway of chitin hydrolysis is preferred by soil microbial communities has previously been unknown. Supplementation of chitin stimulated microbial activity under oxic and anoxic conditions in agricultural soil slurries, whereas chitosan had no effect. Thus, the soil microbial community likely was more adapted to chitin as a substrate. In addition, this finding suggested that direct hydrolysis of chitin was preferred to the pathway that starts with deacetylation. Chitin was apparently degraded by aerobic respiration, ammonification, and nitrification to carbon dioxide and nitrate under oxic conditions. When oxygen was absent, fermentation products (acetate, butyrate, propionate, hydrogen, carbon dioxide) and ammonia were detected, suggesting that butyric and propionic acid fermentation were along with ammonification likely responsible for apparent anaerobic chitin degradation. In total, 42 different chiA genotypes were detected of which twenty were novel at an amino acid sequence dissimilarity of >50%. Various chiA genotypes responded to chitin supplementation and affiliated with a novel deep-branching bacterial chiA genotype (anoxic conditions), genotypes of Beta- and Gammaproteobacteria (oxic and anoxic conditions), and Planctomycetes (oxic conditions). Thus, this study provides evidence that detected chitinolytic bacteria were catabolically diverse and occupied different ecological niches with regard to oxygen availability enabling chitin degradation under various redox conditions at the level of the community.

NC10 Bacteria in a Marine Oxygen Minimum Zone

NASA Astrophysics Data System (ADS)

Padilla, C. C.; Bristow, L. A.; Benson, C. R.; Sarode, N. D.; Girguis, P. R.; Glass, J. B.; DiChristina, T. J.; Thamdrup, B.; Stewart, F. J.

2014-12-01

Marine oxygen minimum zones (OMZs) are key regions of nitrogen cycling and nitrogen loss as N2. The potential for methane cycling to influence OMZ nitrogen budgets remains largely unknown. The anaerobic oxidation of methane (AOM) coupled to nitrite or nitrate reduction has been shown to be a potential source of methane consumption, N loss, and oxygen production in freshwater sediments, but has not been described for marine pelagic environments. Nitrite-dependent AOM is performed by bacteria of the candidate division NC10 through an intra-aerobic pathway involving the dismutation of nitric oxide to O2 and N2. We explored the potential that NC10-like bacteria are present and active in the anoxic, nitrite-rich OMZ of the Eastern Tropical North Pacific. Community transcriptome sequencing confirmed the expression of genes with top matches to the NC10 bacterium 'Candidatus Methylomirabilis oxyfera.' NC10-like transcripts increased in relative abundance with depth into the anoxic OMZ core and included genes of aerobic methanotrophy and denitrification, as well as high numbers of transcripts matching norZ nitric oxide reductase, hypothesized to play a role in the O2-yielding dismutation reaction. Phylogenetic analysis of OMZ particulate methane monooxygenase (pmoA) and 16S rRNA gene sequences recovered by PCR revealed multiple clades of NC10 phylotypes in the OMZ. Preliminary data from OMZ enrichments revealed methane-dependent nitrite consumption, but further characterization is required to identify the pathways and organisms mediating this process. These findings expand the known environmental range of NC10 and suggest the possibility of previously uncharacterized linkages between OMZ nitrogen and methane cycles.

Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic–Anoxic Interface of the Congo Deep-Sea Fan

PubMed Central

Bessette, Sandrine; Moalic, Yann; Gautey, Sébastien; Lesongeur, Françoise; Godfroy, Anne; Toffin, Laurent

2017-01-01

Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3–5% organic carbon). This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB) communities at the oxic–anoxic interface of sedimentary habitats by using fluorescence in situ hybridization and comparative sequence analysis of particulate mono-oxygenase (pmoA) genes. Our findings revealed that sedimentary habitats of the recent lobe complex hosted type I and type II MOB cells and comparisons of pmoA community compositions showed variations among the different organic-rich habitats. Furthermore, the pmoA lineages were taxonomically more diverse compared to methane seep environments and were related to those found at cold seeps. Surprisingly, MOB phylogenetic lineages typical of terrestrial environments were observed at such water depth. In contrast, MOB cells or pmoA sequences were not detected at the previous lobe complex that is disconnected from the Congo River inputs. PMID:28487684

Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic-Anoxic Interface of the Congo Deep-Sea Fan.

PubMed

Bessette, Sandrine; Moalic, Yann; Gautey, Sébastien; Lesongeur, Françoise; Godfroy, Anne; Toffin, Laurent

2017-01-01

Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3-5% organic carbon). This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB) communities at the oxic-anoxic interface of sedimentary habitats by using fluorescence in situ hybridization and comparative sequence analysis of particulate mono-oxygenase ( pmoA ) genes. Our findings revealed that sedimentary habitats of the recent lobe complex hosted type I and type II MOB cells and comparisons of pmoA community compositions showed variations among the different organic-rich habitats. Furthermore, the pmoA lineages were taxonomically more diverse compared to methane seep environments and were related to those found at cold seeps. Surprisingly, MOB phylogenetic lineages typical of terrestrial environments were observed at such water depth. In contrast, MOB cells or pmoA sequences were not detected at the previous lobe complex that is disconnected from the Congo River inputs.

The first metazoa living in permanently anoxic conditions

PubMed Central

2010-01-01

Background Several unicellular organisms (prokaryotes and protozoa) can live under permanently anoxic conditions. Although a few metazoans can survive temporarily in the absence of oxygen, it is believed that multi-cellular organisms cannot spend their entire life cycle without free oxygen. Deep seas include some of the most extreme ecosystems on Earth, such as the deep hypersaline anoxic basins of the Mediterranean Sea. These are permanently anoxic systems inhabited by a huge and partly unexplored microbial biodiversity. Results During the last ten years three oceanographic expeditions were conducted to search for the presence of living fauna in the sediments of the deep anoxic hypersaline L'Atalante basin (Mediterranean Sea). We report here that the sediments of the L'Atalante basin are inhabited by three species of the animal phylum Loricifera (Spinoloricus nov. sp., Rugiloricus nov. sp. and Pliciloricus nov. sp.) new to science. Using radioactive tracers, biochemical analyses, quantitative X-ray microanalysis and infrared spectroscopy, scanning and transmission electron microscopy observations on ultra-sections, we provide evidence that these organisms are metabolically active and show specific adaptations to the extreme conditions of the deep basin, such as the lack of mitochondria, and a large number of hydrogenosome-like organelles, associated with endosymbiotic prokaryotes. Conclusions This is the first evidence of a metazoan life cycle that is spent entirely in permanently anoxic sediments. Our findings allow us also to conclude that these metazoans live under anoxic conditions through an obligate anaerobic metabolism that is similar to that demonstrated so far only for unicellular eukaryotes. The discovery of these life forms opens new perspectives for the study of metazoan life in habitats lacking molecular oxygen. PMID:20370908

The first metazoa living in permanently anoxic conditions.

PubMed

Danovaro, Roberto; Dell'Anno, Antonio; Pusceddu, Antonio; Gambi, Cristina; Heiner, Iben; Kristensen, Reinhardt Møbjerg

2010-04-06

Several unicellular organisms (prokaryotes and protozoa) can live under permanently anoxic conditions. Although a few metazoans can survive temporarily in the absence of oxygen, it is believed that multi-cellular organisms cannot spend their entire life cycle without free oxygen. Deep seas include some of the most extreme ecosystems on Earth, such as the deep hypersaline anoxic basins of the Mediterranean Sea. These are permanently anoxic systems inhabited by a huge and partly unexplored microbial biodiversity. During the last ten years three oceanographic expeditions were conducted to search for the presence of living fauna in the sediments of the deep anoxic hypersaline L'Atalante basin (Mediterranean Sea). We report here that the sediments of the L'Atalante basin are inhabited by three species of the animal phylum Loricifera (Spinoloricus nov. sp., Rugiloricus nov. sp. and Pliciloricus nov. sp.) new to science. Using radioactive tracers, biochemical analyses, quantitative X-ray microanalysis and infrared spectroscopy, scanning and transmission electron microscopy observations on ultra-sections, we provide evidence that these organisms are metabolically active and show specific adaptations to the extreme conditions of the deep basin, such as the lack of mitochondria, and a large number of hydrogenosome-like organelles, associated with endosymbiotic prokaryotes. This is the first evidence of a metazoan life cycle that is spent entirely in permanently anoxic sediments. Our findings allow us also to conclude that these metazoans live under anoxic conditions through an obligate anaerobic metabolism that is similar to that demonstrated so far only for unicellular eukaryotes. The discovery of these life forms opens new perspectives for the study of metazoan life in habitats lacking molecular oxygen.

Metabolic Strategies in Energy-Limited Microbial Communities in the Anoxic Subsurface (Frasassi Cave System, Italy)

NASA Astrophysics Data System (ADS)

McCauley, R. L.; Jones, D. S.; Schaperdoth, I.; Steinberg, L.; Macalady, J. L.

2010-12-01

Two major sources of energy, light and chemical potential, are available to microorganisms. However, energy is not always abundant and is often a limiting factor in microbial survival and replication. The anoxic, terrestrial subsurface offers a unique opportunity to study microorganisms and their potentially novel metabolic strategies that are relevant for understanding biogeochemistry and biosignatures as related to the non-photosynthetic, energy-limited environments on the modern and ancient Earth and elsewhere in the solar system. Geochemical data collected in a remote stratified lake 600 m below ground surface in the sulfidic Frasassi cave system (Italy) suggest that little redox energy is available for life, consistent with low signal from domain-specific FISH probes. The carbon isotope signatures of biofilms (-33‰) and DIC (-9‰) in the anoxic water suggest in situ production by lithoautotrophs using RuBisCO. 16S rDNA libraries constructed from the biofilm are dominated by diverse sulfate reducing bacteria. The remaining bacterial and archaeal clones affiliate with more than 11 major uncultivated or novel prokaryotic lineages. Diverse dsrAB gene sequences are consistent with high sulfate concentrations and undetectable or extremely low oxygen, nitrate, and iron concentrations. However, the electron donor for sulfate reduction is unclear. Methane is detectable in the anoxic water although no 16S rDNA sequences associated with known methanogens or anaerobic methane oxidizers were retrieved. mcrA gene sequences retrieved from the biofilm by cloning are not related to cultivated methanogens or to known anaerobic methane oxidizers. Non-purgable organic carbon (NPOC) is below detection limits (i.e. <42 μM acetate) suggesting that alternative electron donors or novel metabolisms may be important. A sample collected by cave divers in October 2009 was pyrosequenced at the Pennsylvania State University Genomics Core Facility using Titanium chemistry (454 Life

Bacterial Swarms Recruit Cargo Bacteria To Pave the Way in Toxic Environments

PubMed Central

Finkelshtein, Alin; Roth, Dalit

2015-01-01

ABSTRACT Swarming bacteria are challenged by the need to invade hostile environments. Swarms of the flagellated bacterium Paenibacillus vortex can collectively transport other microorganisms. Here we show that P. vortex can invade toxic environments by carrying antibiotic-degrading bacteria; this transport is mediated by a specialized, phenotypic subpopulation utilizing a process not dependent on cargo motility. Swarms of beta-lactam antibiotic (BLA)-sensitive P. vortex used beta-lactamase-producing, resistant, cargo bacteria to detoxify BLAs in their path. In the presence of BLAs, both transporter and cargo bacteria gained from this temporary cooperation; there was a positive correlation between BLA resistance and dispersal. P. vortex transported only the most beneficial antibiotic-resistant cargo (including environmental and clinical isolates) in a sustained way. P. vortex displayed a bet-hedging strategy that promoted the colonization of nontoxic niches by P. vortex alone; when detoxifying cargo bacteria were not needed, they were lost. This work has relevance for the dispersal of antibiotic-resistant microorganisms and for strategies for asymmetric cooperation with agricultural and medical implications. PMID:25968641

Influence of anoxic pore water dissolved organic matter on the fate and transport of hydrophobic organic pollutants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hunchak-Kariouk, K.

1992-01-01

Pore water dissolved organic matter is an overlooked pool of organic matter important to the environmental fate of hydrophobic organic pollutants. The association of polychlorinated biphenyls, polyaromatic hydrocarbons and chlorinated pesticides with pore water dissolved organic matter influences their distribution and mobility within the bottom sediment environment. Steep physical, biological and chemical gradients at the sediment/water interface isolate the pore water and create unique conditions within the sediment. This study indicates that any disturbance of this environment will alter the distribution and mobility of organic pollutants by changing their association to the pore water dissolved organic matter. A small volumemore » closed equilibration method was developed to measure the solubility enhancement of 2,2' 4,4'-tetrachlorobiphenyl (TeCB) by natural dissolved organic matter. Chemical coated micro-glass beads were equilibrated with anoxic and laboratory aerated (oxic) pore water samples in flame sealed ampules. The TeCB enhanced solubilities were used to determine the pore water dissolved organic matter partition coefficient, K[sub pwdom]. The measured TeCB solubility and K[sub pwdom] were much smaller for anoxic than oxic pore waters. The dissolved organic matter sorptive capacity for the TeCB increased as the water was aerated. This change is attributed to coagulative fractionation and structural changes of the pore water dissolved organic matter during aeration and was characterized by differences in the dissolved organic matter concentration, UV absorption at 254 nm, interfacial surface tension, and sorption capacity of molecular weight fractions of anoxic and oxic pore water dissolved organic matter. The increase in partitioning indicates that there will be an increase in the mobility of the TeCB as an anoxic bottom sediment environment is disturbed and aerated.« less

Formation of methane and carbon dioxide from dimethylselenide in anoxic sediments and by a methanogenic bacterium

USGS Publications Warehouse

Oremland, Ronald S.; Zehr, Jon P.

1986-01-01

Anaerobic San Francisco Bay salt marsh sediments rapidly metabolized [14C]dimethylselenide (DMSe) to 14CH4 and 14CO2. Addition of selective inhibitors (2-bromoethanesulfonic acid or molybdate) to these sediments indicated that both methanogenic and sulfate-respiring bacteria could degrade DMSe to gaseous products. However, sediments taken from the selenium-contaminated Kesterson Wildlife Refuge produced only 14CO2 from [14C]DMSe, implying that methanogens were not important in the Kesterson samples. A pure culture of a dimethylsulfide (DMS)-grown methylotrophic methanogen converted [14C]DMSe to 14CH4 and14CO2. However, the organism could not grow on DMSe. Addition of DMS to either sediments or the pure culture retarded the metabolism of DMSe. This effect appeared to be caused by competitive inhibition, thereby indicating a common enzyme system for DMS and DMSe metabolism. DMSe appears to be degraded as part of the DMS pool present in anoxic environments. These results suggest that methylotrophic methanogens may demethylate methylated forms of other metals and metalloids found in nature.

Diversity of Bacillus-like organisms isolated from deep-sea hypersaline anoxic sediments

PubMed Central

Sass, Andrea M; McKew, Boyd A; Sass, Henrik; Fichtel, Jörg; Timmis, Kenneth N; McGenity, Terry J

2008-01-01

Background The deep-sea, hypersaline anoxic brine lakes in the Mediterranean are among the most extreme environments on earth, and in one of them, the MgCl2-rich Discovery basin, the presence of active microbes is equivocal. However, thriving microbial communities have been detected especially in the chemocline between deep seawater and three NaCl-rich brine lakes, l'Atalante, Bannock and Urania. By contrast, the microbiota of these brine-lake sediments remains largely unexplored. Results Eighty nine isolates were obtained from the sediments of four deep-sea, hypersaline anoxic brine lakes in the Eastern Mediterranean Sea: l'Atalante, Bannock, Discovery and Urania basins. This culture collection was dominated by representatives of the genus Bacillus and close relatives (90% of all isolates) that were investigated further. Physiological characterization of representative strains revealed large versatility with respect to enzyme activities or substrate utilization. Two third of the isolates did not grow at in-situ salinities and were presumably present as endospores. This is supported by high numbers of endospores in Bannock, Discovery and Urania basins ranging from 3.8 × 105 to 1.2 × 106 g-1 dw sediment. However, the remaining isolates were highly halotolerant growing at salinities of up to 30% NaCl. Some of the novel isolates affiliating with the genus Pontibacillus grew well under anoxic conditions in sulfidic medium by fermentation or anaerobic respiration using dimethylsulfoxide or trimethylamine N-oxide as electron acceptor. Conclusion Some of the halophilic, facultatively anaerobic relatives of Bacillus appear well adapted to life in this hostile environment and suggest the presence of actively growing microbial communities in the NaCl-rich, deep-sea brine-lake sediments. PMID:18541011

Metabolism in anoxic permeable sediments is dominated by eukaryotic dark fermentation

PubMed Central

Bourke, Michael F; Marriott, Philip J.; Glud, Ronnie N.; Hasler-Sheetal, Harald; Kamalanathan, Manoj; Beardall, John; Greening, Chris; Cook, Perran L.M.

2016-01-01

Permeable sediments are common across continental shelves and are critical contributors to marine biogeochemical cycling. Organic matter in permeable sediments is dominated by microalgae, which as eukaryotes have different anaerobic metabolic pathways to prokaryotes such as bacteria and archaea. Here we present analyses of flow-through reactor experiments showing that dissolved inorganic carbon is produced predominantly as a result of anaerobic eukaryotic metabolic activity. In our experiments, anaerobic production of dissolved inorganic carbon was consistently accompanied by large dissolved H2 production rates, suggesting the presence of fermentation. The production of both dissolved inorganic carbon and H2 persisted following administration of broad spectrum bactericidal antibiotics, but ceased following treatment with metronidazole. Metronidazole inhibits the ferredoxin/hydrogenase pathway of fermentative eukaryotic H2 production, suggesting that pathway as the source of H2 and dissolved inorganic carbon production. Metabolomic analysis showed large increases in lipid production at the onset of anoxia, consistent with documented pathways of anoxic dark fermentation in microalgae. Cell counts revealed a predominance of microalgae in the sediments. H2 production was observed in dark anoxic cultures of diatoms (Fragilariopsis sp.) and a chlorophyte (Pyramimonas) isolated from the study site, substantiating the hypothesis that microalgae undertake fermentation. We conclude that microalgal dark fermentation could be an important energy-conserving pathway in permeable sediments. PMID:28070216

Uranium(IV) adsorption by natural organic matter in anoxic sediments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bone, Sharon E.; Dynes, James J.; Cliff, John

Uranium is an important carbon-free fuel source and environmental contaminant that accumulates in the tetravalent state, U(IV), in anoxic sediments, such as ore deposits, marine basins, and contaminated aquifers. However, little is known about the speciation of U(IV) in low-temperature geochemical environments, inhibiting the development of a conceptual model of U behavior. Until recently, U(IV) was assumed to exist predominantly as the sparingly soluble mineral uraninite (UO 2+x) in anoxic sediments; however, studies now show that this is not often the case. Yet a model of U(IV) speciation in the absence of mineral formation under field-relevant conditions has not yetmore » been developed. Uranium(IV) speciation controls its reactivity, particularly its susceptibility to oxidative mobilization, impacting its distribution and toxicity. Here we show adsorption to organic carbon and organic carbon-coated clays dominate U(IV) speciation in an organic-rich natural substrate under field-relevant conditions. Whereas previous research assumed that U(IV) speciation is dictated by the mode of reduction (i.e., whether reduction is mediated by microbes or by inorganic reductants), our results demonstrate that mineral formation can be diminished in favor of adsorption, regardless of reduction pathway. Projections of U transport and bioavailability, and thus its threat to human and ecosystem health, must consider U(IV) adsorption to organic matter within the sediment environment.« less

Uranium(IV) adsorption by natural organic matter in anoxic sediments

DOE PAGES

Bone, Sharon E.; Dynes, James J.; Cliff, John; ...

2017-01-09

Uranium is an important carbon-free fuel source and environmental contaminant that accumulates in the tetravalent state, U(IV), in anoxic sediments, such as ore deposits, marine basins, and contaminated aquifers. However, little is known about the speciation of U(IV) in low-temperature geochemical environments, inhibiting the development of a conceptual model of U behavior. Until recently, U(IV) was assumed to exist predominantly as the sparingly soluble mineral uraninite (UO 2+x) in anoxic sediments; however, studies now show that this is not often the case. Yet a model of U(IV) speciation in the absence of mineral formation under field-relevant conditions has not yetmore » been developed. Uranium(IV) speciation controls its reactivity, particularly its susceptibility to oxidative mobilization, impacting its distribution and toxicity. Here we show adsorption to organic carbon and organic carbon-coated clays dominate U(IV) speciation in an organic-rich natural substrate under field-relevant conditions. Whereas previous research assumed that U(IV) speciation is dictated by the mode of reduction (i.e., whether reduction is mediated by microbes or by inorganic reductants), our results demonstrate that mineral formation can be diminished in favor of adsorption, regardless of reduction pathway. Projections of U transport and bioavailability, and thus its threat to human and ecosystem health, must consider U(IV) adsorption to organic matter within the sediment environment.« less

Energetics and Application of Heterotrophy in Acetogenic Bacteria.

PubMed

Schuchmann, Kai; Müller, Volker

2016-07-15

Acetogenic bacteria are a diverse group of strictly anaerobic bacteria that utilize the Wood-Ljungdahl pathway for CO2 fixation and energy conservation. These microorganisms play an important part in the global carbon cycle and are a key component of the anaerobic food web. Their most prominent metabolic feature is autotrophic growth with molecular hydrogen and carbon dioxide as the substrates. However, most members also show an outstanding metabolic flexibility for utilizing a vast variety of different substrates. In contrast to autotrophic growth, which is hardly competitive, metabolic flexibility is seen as a key ability of acetogens to compete in ecosystems and might explain the almost-ubiquitous distribution of acetogenic bacteria in anoxic environments. This review covers the latest findings with respect to the heterotrophic metabolism of acetogenic bacteria, including utilization of carbohydrates, lactate, and different alcohols, especially in the model acetogen Acetobacterium woodii Modularity of metabolism, a key concept of pathway design in synthetic biology, together with electron bifurcation, to overcome energetic barriers, appears to be the basis for the amazing substrate spectrum. At the same time, acetogens depend on only a relatively small number of enzymes to expand the substrate spectrum. We will discuss the energetic advantages of coupling CO2 reduction to fermentations that exploit otherwise-inaccessible substrates and the ecological advantages, as well as the biotechnological applications of the heterotrophic metabolism of acetogens. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments.

PubMed

Zhuang, Kai; Izallalen, Mounir; Mouser, Paula; Richter, Hanno; Risso, Carla; Mahadevan, Radhakrishnan; Lovley, Derek R

2011-02-01

The advent of rapid complete genome sequencing, and the potential to capture this information in genome-scale metabolic models, provide the possibility of comprehensively modeling microbial community interactions. For example, Rhodoferax and Geobacter species are acetate-oxidizing Fe(III)-reducers that compete in anoxic subsurface environments and this competition may have an influence on the in situ bioremediation of uranium-contaminated groundwater. Therefore, genome-scale models of Geobacter sulfurreducens and Rhodoferax ferrireducens were used to evaluate how Geobacter and Rhodoferax species might compete under diverse conditions found in a uranium-contaminated aquifer in Rifle, CO. The model predicted that at the low rates of acetate flux expected under natural conditions at the site, Rhodoferax will outcompete Geobacter as long as sufficient ammonium is available. The model also predicted that when high concentrations of acetate are added during in situ bioremediation, Geobacter species would predominate, consistent with field-scale observations. This can be attributed to the higher expected growth yields of Rhodoferax and the ability of Geobacter to fix nitrogen. The modeling predicted relative proportions of Geobacter and Rhodoferax in geochemically distinct zones of the Rifle site that were comparable to those that were previously documented with molecular techniques. The model also predicted that under nitrogen fixation, higher carbon and electron fluxes would be diverted toward respiration rather than biomass formation in Geobacter, providing a potential explanation for enhanced in situ U(VI) reduction in low-ammonium zones. These results show that genome-scale modeling can be a useful tool for predicting microbial interactions in subsurface environments and shows promise for designing bioremediation strategies.

Sulphur bacteria mediated formation of Palaeoproterozoic phosphorites

NASA Astrophysics Data System (ADS)

Joosu, Lauri; Lepland, Aivo; Kirsimäe, Kalle

2014-05-01

Modern phosphorite formation is typically associated with high productivity in upwelling areas where apatite (Ca-phosphate) precipitation is mediated by sulphur oxidising bacteria [1]. They inhabit the oxic/anoxic interface within the upper few centimetres of sediment column, accumulating phosphate in their cells under oxic conditions and releasing it rapidly when conditions become anoxic. Sulphur bacteria are known to live in close association with a consortium of anaerobic methane oxidising archaea and syntrophic sulphate-reducing bacteria. Paleoproterozoic, c. 2.0 Ga Zaonega Formation in Karelia, Russia contains several P-rich intervals in the upper part of 1500 m thick succession of organic-rich sedimentary rocks interlayered with mafic tuffs and lavas. Apatite in these P-rich intervals forms impure laminae, lenses and round-oval nodules which diameters typically range from 300 to 1000 μm. Individual apatite particles in P-rich laminae and nodules commonly occur as cylinders that are 1-8 μm long and have diameters of 0.5-4 μm. Cross-sections of best preserved cylindrical apatite particles reveal a thin outer rim whereas the internal parts consist of small anhedral elongated crystallites, intergrown with carbonaceous material. During recrystallization the outer rim thickens towards interior and cylinders may attain hexagonal crystal habit, but their size and shape remains largely unchanged [2]. The sizes of Zaonega nodules are similar to giant sulphide-oxidising bacteria known from modern and ancient settings [3, 4]. Individual apatite cylinders and aggregates have shapes and sizes similar to the methanotrophic archaea that inhabit microbial mats in modern seep/vent areas where they operate in close associations with sulphur-oxidising microbial communities [5]. Seep/vent influence during the Zaonega phosphogenesis is indicated by variable, though positive Eu anomaly, expected in magmatically active sedimentary environment experiencing several lava flows

Assessment of the endogenous respiration rate and the observed biomass yield for methanol-fed denitrifying bacteria under anoxic and aerobic conditions.

PubMed

Alikhani, Jamal; Al-Omari, Ahmed; De Clippeleir, Haydee; Murthy, Sudhir; Takacs, Imre; Massoudieh, Arash

2017-01-01

In this study, the endogenous respiration rate and the observed biomass yield of denitrifying methylotrophic biomass were estimated through measuring changes in denitrification rates (DNR) as a result of maintaining the biomass under methanol deprived conditions. For this purpose, activated sludge biomass from a full-scale wastewater treatment plant was kept in 10-L batch reactors for 8 days under fully aerobic and anoxic conditions at 20 °C without methanol addition. To investigate temperature effects, another biomass sample was placed under starvation conditions over a period of 10 days under aerobic conditions at 25 °C. A series of secondary batch tests were conducted to measure DNR and observed biomass yields. The decline in DNR over the starvation period was used as a surrogate to biomass decay rate in order to infer the endogenous respiration rates of the methylotrophs. The regression analysis on the declining DNR data shows 95% confidence intervals of 0.130 ± 0.017 day -1 for endogenous respiration rate under aerobic conditions at 20 °C, 0.102 ± 0.013 day -1 under anoxic conditions at 20 °C, and 0.214 ± 0.044 day -1 under aerobic conditions at 25 °C. Results indicated that the endogenous respiration rate of methylotrophs is 20% slower under anoxic conditions than under aerobic conditions, and there is a significant temperature dependency, with an Arrhenius coefficient of 1.10. The observed biomass yield value showed an increasing trend from approximately 0.2 to 0.6 when the starvation time increased from 0 to 10 days.

Isolation of heterotrophic diazotrophic bacteria from estuarine surface waters.

PubMed

Farnelid, Hanna; Harder, Jens; Bentzon-Tilia, Mikkel; Riemann, Lasse

2014-10-01

The wide distribution of diverse nitrogenase (nifH) genes affiliated with those of heterotrophic bacteria in marine and estuarine waters indicates ubiquity and an ecologically relevant role for heterotrophic N2 -fixers (diazotrophs) in aquatic nitrogen (N) cycling. However, the lack of cultivated representatives currently precludes an evaluation of their N2 -fixing capacity. In this study, microoxic or anoxic N-free media were inoculated with estuarine Baltic Sea surface water to select for N2 -fixers. After visible growth and isolation of single colonies on oxic plates or in anoxic agar tubes, nifH gene amplicons were obtained from 64 strains and nitrogenase activity, applying the acetylene reduction assay, was confirmed for 40 strains. Two strains, one Gammaproteobacterium affiliated with Pseudomonas and one Alphaproteobacterium affiliated with Rhodopseudomonas were shown to represent established members of the indigenous diazotrophic community in the Baltic Sea, with abundances of up to 7.9 × 10(4) and 4.7 × 10(4)  nifH copies l(-1) respectively. This study reports media for successful isolation of heterotrophic diazotrophs. The applied methodology and the obtained strains will facilitate future identification of factors controlling heterotrophic diazotrophic activity in aquatic environments, which is a prerequisite for understanding and evaluating their ecology and contribution to N cycling at local and regional scales. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Identification of Bacteria Potentially Responsible for Oxic and Anoxic Sulfide Oxidation in Biofilters of a Recirculating Mariculture System

PubMed Central

Cytryn, Eddie; van Rijn, Jaap; Schramm, Andreas; Gieseke, Armin; de Beer, Dirk; Minz, Dror

2005-01-01

Bacteria presumably involved in oxygen- or nitrate-dependent sulfide oxidation in the biofilters of a recirculating marine aquaculture system were identified using a new application of reverse transcription-PCR denaturing gradient gel electrophoresis (DGGE) analysis termed differential-transcription (DT)-DGGE. Biofilter samples were incubated in various concentrations of sulfide or thiosulfate (0 to 5 mM) with either oxygen or nitrate as the sole electron acceptor. Before and after short-term incubations (10 to 20 h), total DNA and RNA were extracted, and a 550-bp fragment of the 16S rRNA genes was PCR amplified either directly or after reverse transcription. DGGE analysis of DNA showed no significant change of the original microbial consortia upon incubation. In contrast, DGGE of cDNA revealed several phylotypes whose relative band intensities markedly increased or decreased in response to certain incubation conditions, indicating enhanced or suppressed rRNA transcription and thus implying metabolic activity under these conditions. Specifically, species of the gammaproteobacterial genus Thiomicrospira and phylotypes related to symbiotic sulfide oxidizers could be linked to oxygen-dependent sulfide oxidation, while members of the Rhodobacteraceae (genera Roseobacter, Rhodobacter, and Rhodobium) were putatively active in anoxic, nitrate-dependent sulfide oxidation. For all these organisms, the physiology of their closest cultured relatives matches their DT-DGGE-inferred function. In addition, higher band intensities following exposure to 5 mM sulfide and nitrate were observed for Thauera-, Hydrogenophaga-, and Dethiosulfovibrio-like phylotypes. For these genera, nitrate-dependent sulfide oxidation has not been documented previously and therefore DT-DGGE might indicate a higher relative tolerance to high sulfide concentrations than that of other community members. We anticipate that DT-DGGE will be of general use in tracing functionally equivalent yet

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

PubMed Central

Zhuang, Kai; Izallalen, Mounir; Mouser, Paula; Richter, Hanno; Risso, Carla; Mahadevan, Radhakrishnan; Lovley, Derek R

2011-01-01

The advent of rapid complete genome sequencing, and the potential to capture this information in genome-scale metabolic models, provide the possibility of comprehensively modeling microbial community interactions. For example, Rhodoferax and Geobacter species are acetate-oxidizing Fe(III)-reducers that compete in anoxic subsurface environments and this competition may have an influence on the in situ bioremediation of uranium-contaminated groundwater. Therefore, genome-scale models of Geobacter sulfurreducens and Rhodoferax ferrireducens were used to evaluate how Geobacter and Rhodoferax species might compete under diverse conditions found in a uranium-contaminated aquifer in Rifle, CO. The model predicted that at the low rates of acetate flux expected under natural conditions at the site, Rhodoferax will outcompete Geobacter as long as sufficient ammonium is available. The model also predicted that when high concentrations of acetate are added during in situ bioremediation, Geobacter species would predominate, consistent with field-scale observations. This can be attributed to the higher expected growth yields of Rhodoferax and the ability of Geobacter to fix nitrogen. The modeling predicted relative proportions of Geobacter and Rhodoferax in geochemically distinct zones of the Rifle site that were comparable to those that were previously documented with molecular techniques. The model also predicted that under nitrogen fixation, higher carbon and electron fluxes would be diverted toward respiration rather than biomass formation in Geobacter, providing a potential explanation for enhanced in situ U(VI) reduction in low-ammonium zones. These results show that genome-scale modeling can be a useful tool for predicting microbial interactions in subsurface environments and shows promise for designing bioremediation strategies. PMID:20668487

Distribution of hydrocarbon-degrading bacteria in the soil environment and their contribution to bioremediation.

PubMed

Fukuhara, Yuki; Horii, Sachie; Matsuno, Toshihide; Matsumiya, Yoshiki; Mukai, Masaki; Kubo, Motoki

2013-05-01

A real-time PCR quantification method for indigenous hydrocarbon-degrading bacteria (HDB) carrying the alkB gene in the soil environment was developed to investigate their distribution in soil. The detection limit of indigenous HDB by the method was 1 × 10(6) cells/g-soil. The indigenous HDB were widely distributed throughout the soil environment and ranged from 3.7 × 10(7) to 5.0 × 10(8) cells/g-soil, and the ratio to total bacteria was 0.1-4.3 %. The dynamics of total bacteria, indigenous HDB, and Rhodococcus erythropolis NDKK6 (carrying alkB R2) during bioremediation were analyzed. During bioremediation with an inorganic nutrient treatment, the numbers of these bacteria were slightly increased. The numbers of HDB (both indigenous bacteria and strain NDKK6) were gradually decreased from the middle stage of bioremediation. Meanwhile, the numbers of these bacteria were highly increased and were maintained during bioremediation with an organic nutrient. The organic treatment led to activation of not only the soil bacteria but also the HDB, so an efficient bioremediation was carried out.

Characteristics of airborne bacteria in Mumbai urban environment.

PubMed

Gangamma, S

2014-08-01

Components of biological origin constitute small but a significant proportion of the ambient airborne particulate matter (PM). However, their diversity and role in proinflammatory responses of PM are not well understood. The present study characterizes airborne bacterial species diversity in Mumbai City and elucidates the role of bacterial endotoxin in PM induced proinflammatory response in ex vivo. Airborne bacteria and endotoxin samples were collected during April-May 2010 in Mumbai using six stage microbial impactor and biosampler. The culturable bacterial species concentration was measured and factors influencing the composition were identified by principal component analysis (PCA). The biosampler samples were used to stimulate immune cells in whole blood assay. A total of 28 species belonging to 17 genera were identified. Gram positive and spore forming groups of bacteria dominated the airborne culturable bacterial concentration. The study indicated the dominance of spore forming and human or animal flora derived pathogenic/opportunistic bacteria in the ambient air environment. Pathogenic and opportunistic species of bacteria were also present in the samples. TNF-α induction by PM was reduced (35%) by polymyxin B pretreatment and this result was corroborated with the results of blocking endotoxin receptor cluster differentiation (CD14). The study highlights the importance of airborne biological particles and suggests need of further studies on biological characterization of ambient PM. Copyright © 2014 Elsevier B.V. All rights reserved.

Photochemical synthesis of biomolecules under anoxic conditions

NASA Technical Reports Server (NTRS)

Folsome, C.; Brittain, A.; Zelko, M.

1983-01-01

The long-wavelength UV anoxic photosynthesis of uracil, various sugars (including deoxyribose and glycoaldehyde), amino acids, and other organic photoproducts is reported. The reactions were conducted in a mixture of water, calcium carbonate, hydrazine, and formaldehyde which were subjected to 24 hr or 72 hr radiation. Product yields were greatest when the hydrazine/formaldehyde ratio was one, and when the reactant concentrations were low. These data suggest that organic products can be formed in variety from those amounts of formaldehyde and hydazine precursors which are themselves formed under anoxic UV photochemical conditions.

Phylogenetic Diversity of Archaea and Bacteria in the Anoxic Zone of a Meromictic Lake (Lake Pavin, France)▿ †

PubMed Central

Lehours, Anne-Catherine; Evans, Paul; Bardot, Corinne; Joblin, Keith; Gérard, Fonty

2007-01-01

The compositions of archaeal and bacterial populations at different depths (60 m [mixolimnion-chemocline interface], 70 m [chemocline-subchemocline interface], 90 m, and 92 m [the water-sediment interface]) in the anoxic zone of the water column in Lake Pavin, a freshwater permanently stratified mountain lake in France, were determined. Phylogenetic trees were constructed from sequences to assess archaeal and bacterial diversity at the four sites. PMID:17261512

Surveying N2O-producing pathways in bacteria.

PubMed

Stein, Lisa Y

2011-01-01

Nitrous oxide (N(2)O) is produced by bacteria as an intermediate of both dissimilatory and detoxification pathways under a range of oxygen levels, although the majority of N(2)O is released in suboxic to anoxic environments. N(2)O production under physiologically relevant conditions appears to require the reduction of nitric oxide (NO) produced from the oxidation of hydroxylamine (nitrification), reduction of nitrite (denitrification), or by host cells of pathogenic bacteria. In a single bacterial isolate, N(2)O-producing pathways can be complex, overlapping, involve multiple enzymes with the same function, and require multiple layers of regulatory machinery. This overview discusses how to identify known N(2)O-producing inventory and regulatory sequences within bacterial genome sequences and basic physiological approaches for investigating the function of that inventory. A multitude of review articles have been published on individual enzymes, pathways, regulation, and environmental significance of N(2)O-production encompassing a large diversity of bacterial isolates. The combination of next-generation deep sequencing platforms, emerging proteomics technologies, and basic microbial physiology can be used to expand what is known about N(2)O-producing pathways in individual bacterial species to discover novel inventory and unifying features of pathways. A combination of approaches is required to understand and generalize the function and control of N(2)O production across a range of temporal and spatial scales within natural and host environments. Copyright © 2011 Elsevier Inc. All rights reserved.

The isotopic composition of authigenic chromium in anoxic marine sediments: A case study from the Cariaco Basin

NASA Astrophysics Data System (ADS)

Reinhard, Christopher T.; Planavsky, Noah J.; Wang, Xiangli; Fischer, Woodward W.; Johnson, Thomas M.; Lyons, Timothy W.

2014-12-01

Chromium (Cr) isotopes are an emerging proxy for tracking redox processes at the Earth's surface. However, there has been limited exploration of the Cr isotope record of modern and recent marine sediments. The basic inorganic chemistry of Cr suggests that anoxic marine basins should factor prominently in the global Cr cycle and that sediments deposited within anoxic basins may offer a valuable Cr isotope archive throughout Earth's history. Here, we present δ53Cr data from sediments of the Cariaco Basin, Venezuela-a 'type' environment for large, perennially anoxic basins with a relatively strong hydrological connection to the global oceans. We document a marked positive shift in bulk δ53Cr values following the termination of the Last Glacial Maximum, followed by relative stasis. Based on a suite of independent redox proxies, this transition marks a switch from oxic to persistently anoxic and sulfidic (euxinic) depositional conditions within the basin. We find good agreement between two independent approaches toward estimating the δ53Cr composition of authigenic Cr in euxinic Cariaco Basin sediments and that these estimates are very similar to the δ53Cr composition of modern open Atlantic Ocean seawater. These data, together with considerations of reaction kinetics and mass balance within the Cariaco Basin, are consistent with the hypothesis that anoxic marine settings can serve as a chemical archive of first-order trends in seawater δ53Cr composition. Additionally, the Cariaco Basin data suggest that there has been secular stability in the average δ53Cr value of Atlantic seawater over the last ∼15 kyr.

Microeukaryote Community Patterns along an O2/H2S Gradient in a Supersulfidic Anoxic Fjord (Framvaren, Norway)†

PubMed Central

Behnke, Anke; Bunge, John; Barger, Kathryn; Breiner, Hans-Werner; Alla, Victoria; Stoeck, Thorsten

2006-01-01

To resolve the fine-scale architecture of anoxic protistan communities, we conducted a cultivation-independent 18S rRNA survey in the superanoxic Framvaren Fjord in Norway. We generated three clone libraries along the steep O2/H2S gradient, using the multiple-primer approach. Of 1,100 clones analyzed, 753 proved to be high-quality protistan target sequences. These sequences were grouped into 92 phylotypes, which displayed high protistan diversity in the fjord (17 major eukaryotic phyla). Only a few were closely related to known taxa. Several sequences were dissimilar to all previously described sequences and occupied a basal position in the inferred phylogenies, suggesting that the sequences recovered were derived from novel, deeply divergent eukaryotes. We detected sequence clades with evolutionary importance (for example, clades in the euglenozoa) and clades that seem to be specifically adapted to anoxic environments, challenging the hypothesis that the global dispersal of protists is uniform. Moreover, with the detection of clones affiliated with jakobid flagellates, we present evidence that primitive descendants of early eukaryotes are present in this anoxic environment. To estimate sample coverage and phylotype richness, we used parametric and nonparametric statistical methods. The results show that although our data set is one of the largest published inventories, our sample missed a substantial proportion of the protistan diversity. Nevertheless, statistical and phylogenetic analyses of the three libraries revealed the fine-scale architecture of anoxic protistan communities, which may exhibit adaptation to different environmental conditions along the O2/H2S gradient. PMID:16672511

Organic geochemistry of the early Toarcian oceanic anoxic event in Hawsker Bottoms, Yorkshire, England

NASA Astrophysics Data System (ADS)

French, K. L.; Sepúlveda, J.; Trabucho-Alexandre, J.; Gröcke, D. R.; Summons, R. E.

2014-03-01

A comprehensive organic geochemical investigation of the Hawsker Bottoms outcrop section in Yorkshire, England has provided new insights about environmental conditions leading into and during the Toarcian oceanic anoxic event (T-OAE; ∼183 Ma). Rock-Eval and molecular analyses demonstrate that the section is uniformly within the early oil window. Hydrogen index (HI), organic petrography, polycyclic aromatic hydrocarbon (PAH) distributions, and tricyclic terpane ratios mark a shift to a lower relative abundance of terrigenous organic matter supplied to the sampling locality during the onset of the T-OAE and across a lithological transition. Unlike other ancient intervals of anoxia and extinction, biomarker indices of planktonic community structure do not display major changes or anomalous values. Depositional environment and redox indicators support a shift towards more reducing conditions in the sediment porewaters and the development of a seasonally stratified water column during the T-OAE. In addition to carotenoid biomarkers for green sulfur bacteria (GSB), we report the first occurrence of okenane, a marker of purple sulfur bacteria (PSB), in marine samples younger than ∼1.64 Ga. Based on modern observations, a planktonic source of okenane's precursor, okenone, would require extremely shallow photic zone euxinia (PZE) and a highly restricted depositional environment. However, due to coastal vertical mixing, the lack of planktonic okenone production in modern marine sulfidic environments, and building evidence of okenone production in mat-dwelling Chromatiaceae, we propose a sedimentary source of okenone as an alternative. Lastly, we report the first parallel compound-specific δC13 record in marine- and terrestrial-derived biomarkers across the T-OAE. The δC13 records of short-chain n-alkanes, acyclic isoprenoids, and long-chain n-alkanes all encode negative carbon isotope excursions (CIEs), and together, they support an injection of isotopically light

Assessing carbon and nitrogen removal in a novel anoxic-aerobic cyanobacterial-bacterial photobioreactor configuration with enhanced biomass sedimentation.

PubMed

de Godos, I; Vargas, V A; Guzmán, H O; Soto, R; García, B; García, P A; Muñoz, R

2014-09-15

The carbon and nitrogen removal potential of an innovative anoxic-aerobic photobioreactor configuration operated with both internal and external recyclings was evaluated under different cyanobacterial-bacterial sludge residence times (9-31 days) during the treatment of wastewaters with low C/N ratios. Under optimal operating conditions, the two-stage photobioreactor was capable of providing organic carbon and nitrogen removals over 95% and 90%, respectively. The continuous biomass recycling from the settler resulted in the enrichment and predominance of rapidly-settling cyanobacterial-bacterial flocs and effluent suspended solid concentrations lower than 35 mg VSS L(-1). These flocs exhibited sedimentation rates of 0.28-0.42 m h(-1) but sludge volumetric indexes of 333-430 ml/g. The decoupling between the hydraulic retention time and sludge retention time mediated by the external recycling also avoided the washout of nitrifying bacteria and supported process operation at biomass concentrations of 1000-1500 mg VSS L(-1). The addition of additional NaHCO3 to the process overcame the CO2 limitation resulting from the intense competition for inorganic carbon between cyanobacteria and nitrifying bacteria in the photobioreactor, which supported the successful implementation of a nitrification-denitrification process. Unexpectedly, this nitrification-denitrification process occurred both simultaneously in the photobioreactor alone (as a result of the negligible dissolved oxygen concentrations) and sequentially in the two-stage anoxic-aerobic configuration with internal NO3(-)/NO2(-) recycling. Copyright © 2014 Elsevier Ltd. All rights reserved.

Long-distance electron transfer by cable bacteria in aquifer sediments

PubMed Central

Müller, Hubert; Bosch, Julian; Griebler, Christian; Damgaard, Lars Riis; Nielsen, Lars Peter; Lueders, Tillmann; Meckenstock, Rainer U

2016-01-01

The biodegradation of organic pollutants in aquifers is often restricted to the fringes of contaminant plumes where steep countergradients of electron donors and acceptors are separated by limited dispersive mixing. However, long-distance electron transfer (LDET) by filamentous ‘cable bacteria' has recently been discovered in marine sediments to couple spatially separated redox half reactions over centimeter scales. Here we provide primary evidence that such sulfur-oxidizing cable bacteria can also be found at oxic–anoxic interfaces in aquifer sediments, where they provide a means for the direct recycling of sulfate by electron transfer over 1–2-cm distance. Sediments were taken from a hydrocarbon-contaminated aquifer, amended with iron sulfide and saturated with water, leaving the sediment surface exposed to air. Steep geochemical gradients developed in the upper 3 cm, showing a spatial separation of oxygen and sulfide by 9 mm together with a pH profile characteristic for sulfur oxidation by LDET. Bacterial filaments, which were highly abundant in the suboxic zone, were identified by sequencing of 16S rRNA genes and fluorescence in situ hybridization (FISH) as cable bacteria belonging to the Desulfobulbaceae. The detection of similar Desulfobulbaceae at the oxic–anoxic interface of fresh sediment cores taken at a contaminated aquifer suggests that LDET may indeed be active at the capillary fringe in situ. PMID:27058505

Oxygen intrusion into anoxic fjords leads to increased methylmercury availability

NASA Astrophysics Data System (ADS)

Veiteberg Braaten, Hans Fredrik; Pakhomova, Svetlana; Yakushev, Evgeniy

2013-04-01

Mercury (Hg) appears in the oxic surface waters of the oceans at low levels (sub ng/L). Because inorganic Hg can be methylated into the toxic and bioaccumulative specie methylmercury (MeHg) levels can be high at the top of the marine food chain. Even though marine sea food is considered the main risk driver for MeHg exposure to people most research up to date has focused on Hg methylation processes in freshwater systems. This study identifies the mechanisms driving formation of MeHg during oxygen depletion in fjords, and shows how MeHg is made available in the surface water during oxygen intrusion. Studies of the biogeochemical structure in the water column of the Norwegian fjord Hunnbunn were performed in 2009, 2011 and 2012. In autumn of 2011 mixing flushing events were observed and lead to both positive and negative effects on the ecosystem state in the fjord. The oxygenated water intrusions lead to a decrease of the deep layer concentrations of hydrogen sulfide (H2S), ammonia and phosphate. On the other hand the intrusion also raised the H2S boundary from 8 m to a shallower depth of just 4 m. Following the intrusion was also observed an increase at shallower depths of nutrients combined with a decrease of pH. Before flushing events were observed concentrations of total Hg (TotHg) increased from 1.3 - 1.7 ng/L in the surface layer of the fjord to concentrations ranging from 5.2 ng/L to 6.4 ng/L in the anoxic zone. MeHg increased regularly from 0.04 ng/L in the surface water to a maximum concentration of 5.2 ng/L in the deeper layers. This corresponds to an amount of TotHg present as MeHg ranging from 2.1 % to 99 %. The higher concentrations of MeHg in the deeper layer corresponds to an area where no oxygen is present and concentrations of H2S exceeds 500 µM, suggesting a production of MeHg in the anoxic area as a result of sulphate reducing bacteria activity. After flushing the concentrations of TotHg showed a similar pattern ranging from 0.6 ng/L in the

Nitrate-dependent iron oxidation limits iron transport in anoxic ocean regions

NASA Astrophysics Data System (ADS)

Scholz, Florian; Löscher, Carolin R.; Fiskal, Annika; Sommer, Stefan; Hensen, Christian; Lomnitz, Ulrike; Wuttig, Kathrin; Göttlicher, Jörg; Kossel, Elke; Steininger, Ralph; Canfield, Donald E.

2016-11-01

Iron is an essential element for life on Earth and limits primary production in large parts of the ocean. Oxygen-free continental margin sediments represent an important source of bioavailable iron to the ocean, yet little of the iron released from the seabed reaches the productive sea surface. Even in the anoxic water of oxygen minimum zones, where iron solubility should be enhanced, most of the iron is rapidly re-precipitated. To constrain the mechanism(s) of iron removal in anoxic ocean regions we explored the sediment and water in the oxygen minimum zone off Peru. During our sampling campaign the water column featured two distinct redox boundaries separating oxic from nitrate-reducing (i.e., nitrogenous) water and nitrogenous from weakly sulfidic water. The sulfidic water mass in contact with the shelf sediment contained elevated iron concentrations >300 nM. At the boundary between sulfidic and nitrogenous conditions, iron concentrations dropped sharply to <20 nM coincident with a maximum in particulate iron concentration. Within the iron gradient, we found an increased expression of the key functional marker gene for nitrate reduction (narG). Part of this upregulation was related to the activity of known iron-oxidizing bacteria. Collectively, our data suggest that iron oxidation and removal is induced by nitrate-reducing microbes, either enzymatically through anaerobic iron oxidation or by providing nitrite for an abiotic reaction. Given the important role that iron plays in nitrogen fixation, photosynthesis and respiration, nitrate-dependent iron oxidation likely represents a key-link between the marine biogeochemical cycles of nitrogen, oxygen and carbon.

Acid azo dye remediation in anoxic-aerobic-anoxic microenvironment under periodic discontinuous batch operation: bio-electro kinetics and microbial inventory.

PubMed

Venkata Mohan, S; Suresh Babu, P; Naresh, K; Velvizhi, G; Madamwar, Datta

2012-09-01

Functional behavior of anoxic-aerobic-anoxic microenvironment on azo dye (C.I. Acid black 10B) degradation was evaluated in a periodic discontinuous batch mode operation for 26 cycles. Dye removal efficiency and azo-reductase activity (30.50 ± 1 U) increased with each feeding event until 13th cycle and further stabilized. Dehydrogenase activity also increased gradually and stabilized (2.0 ± 0.2 μg/ml) indicating the stable proton shuttling between metabolic intermediates providing higher number of reducing equivalents towards dye degradation. Voltammetric profiles showed drop in redox catalytic currents during stabilized phase also supports the consumption of reducing equivalents towards dye removal. Change in Tafel slopes, polarization resistance and other bioprocess parameters correlated well with the observed dye removal and biocatalyst behavior. Microbial community analysis documented the involvement of specific organism pertaining to aerobic and facultative functions with heterotrophic and autotrophic metabolism. Integrating anoxic microenvironment with aerobic operation might have facilitated effective dye mineralization due to the possibility of combining redox functions. Copyright © 2012 Elsevier Ltd. All rights reserved.

Bacteria and Archaea in acidic environments and a key to morphological identification

USGS Publications Warehouse

Robbins, E.I.

2000-01-01

Natural and anthropogenic acidic environments are dominated by bacteria and Archaea. As many as 86 genera or species have been identified or isolated from pH <4.5 environments. This paper reviews the worldwide literature and provide tables of morphological characteristics, habitat information and a key for light microscope identification for the non-microbiologist.

Microbiological reduction of Sb(V) in anoxic freshwater sediments

USGS Publications Warehouse

Oremland, Ronald S.; Kulp, Thomas R.; Miller, Laurence G.; Braiotta, Franco; Webb, Samuel M.; Kocar, Benjamin D; Blum, Jodi S.

2014-01-01

Microbiological reduction of millimolar concentrations of Sb(V) to Sb(III) was observed in anoxic sediments from two freshwater settings: (1) a Sb- and As-contaminated mine site (Stibnite Mine) in central Idaho and 2) an uncontaminated suburban lake (Searsville Lake) in the San Francisco Bay Area. Rates of Sb(V) reduction in anoxic sediment microcosms and enrichment cultures were enhanced by amendment with lactate or acetate as electron donors but not by H2, and no reduction occurred in sterilized controls. Addition of 2-14C-acetate to Stibnite Mine microcosms resulted in the production of 14CO2 coupled to Sb(V) reduction, suggesting that this process proceeds by a dissimilatory respiratory pathway in those sediments. Antimony(V) reduction in Searsville Lake sediments was not coupled to acetate mineralization and may be associated with Sb-resistance. The microcosms and enrichment cultures also reduced sulfate, and the precipitation of insoluble Sb(III)-sulfide complexes was a major sink for reduced Sb. The reduction of Sb(V) by Stibnite Mine sediments was inhibited by As(V), suggesting that As(V) is a preferred electron acceptor for the indigenous community. These findings indicate a novel pathway for anaerobic microbiological respiration and suggest that communities capable of reducing high concentrations of Sb(V) commonly occur naturally in the environment.

Anoxic denitrification of BTEX: Biodegradation kinetics and pollutant interactions.

PubMed

Carvajal, Andrea; Akmirza, Ilker; Navia, Daniel; Pérez, Rebeca; Muñoz, Raúl; Lebrero, Raquel

2018-05-15

Anoxic mineralization of BTEX represents a promising alternative for their abatement from O 2 -deprived emissions. However, the kinetics of anoxic BTEX biodegradation and the interactions underlying the treatment of BTEX mixtures are still unknown. An activated sludge inoculum was used for the anoxic abatement of single, dual and quaternary BTEX mixtures, being acclimated prior performing the biodegradation kinetic tests. The Monod model and a Modified Gompertz model were then used for the estimation of the biodegradation kinetic parameters. Results showed that both toluene and ethylbenzene are readily biodegradable under anoxic conditions, whereas the accumulation of toxic metabolites resulted in partial xylene and benzene degradation when present both as single components or in mixtures. Moreover, the supplementation of an additional pollutant always resulted in an inhibitory competition, with xylene inducing the highest degree of inhibition. The Modified Gompertz model provided an accurate fitting for the experimental data for single and dual substrate experiments, satisfactorily representing the antagonistic pollutant interactions. Finally, microbial analysis suggested that the degradation of the most biodegradable compounds required a lower microbial specialization and diversity, while the presence of the recalcitrant compounds resulted in the selection of a specific group of microorganisms. Copyright © 2018 Elsevier Ltd. All rights reserved.

Anoxic biodegradation of triclosan and the removal of its antimicrobial effect in microbial fuel cells.

PubMed

Wang, Lu; Liu, Yulei; Wang, Chao; Zhao, Xiaodan; Mahadeva, Gurumurthy Dummi; Wu, Yicheng; Ma, Jun; Zhao, Feng

2018-02-15

Triclosan (TCS) is an emerging organic contaminant in the environment. Here, the anoxic bio-degradation of TCS in microbial fuel cells (MFCs) was explored. It was found that anoxic biodegradation of TCS could be achieved in MFC, and the removal rate of TCS was accelerated after reactor acclimation. After 7 months of operation, 10mg/L TCS could be removed within 8days in MFCs. Fluorescence microscopy results revealed that the microbe cells in the reactors were intact, and the microbes were in active state. Flow cytometry test showed that the proliferation of inoculated microbe was higher in MFC effluent than that in TCS solution. These data indicate that the biotoxicity of TCS has been largely eliminated after the treatment. The microbial community shift during the TCS degradation process was investigated as well. Species such as Geothrix, Corynebacterium, Sulfobacillus, GOUTA19, Geobacter, Acidithiobacillus and Acinetobacter, which were capable for the degradation of benzene-related and dechlorination of chlorine-containing chemicals, were flourished in the electrode biofilm. They may participate in the biodegradation of TCS. This work provides a new perspective for the anoxic biodegradation of recalcitrant organics, and can be useful for the in-situ bioremediation of environmental pollutants with the removal of their biotoxicity. Copyright © 2017. Published by Elsevier B.V.

Anoxic biodegradation of petroleum hydrocarbons in saline media using denitrifier biogranules.

PubMed

Moussavi, Gholamreza; Shekoohiyan, Sakine; Naddafi, Kazem

2016-07-01

The total petroleum hydrocarbons (TPH) biodegradation was examined using biogranules at different initial TPH concentration and contact time under anoxic condition in saline media. The circular compact biogranules having the average diameter between 2 and 3mm were composed of a dense population of Bacillus spp. capable of biodegrading TPH under anoxic condition in saline media were formed in first step of the study. The biogranules could biodegrade over 99% of the TPH at initial concentration up to 2g/L at the contact time of 22h under anoxic condition in saline media. The maximum TPH biodegradation rate of 2.6 gTPH/gbiomass.d could be obtained at initial TPH concentration of 10g/L. Accordingly, the anoxic biogranulation is a possible and promising technique for high-rate biodegradation of petroleum hydrocarbons in saline media. Copyright © 2016 Elsevier Inc. All rights reserved.

Nitrous oxide production by lithotrophic ammonia-oxidizing bacteria and implications for engineered nitrogen-removal systems.

PubMed

Chandran, Kartik; Stein, Lisa Y; Klotz, Martin G; van Loosdrecht, Mark C M

2011-12-01

Chemolithoautotrophic AOB (ammonia-oxidizing bacteria) form a crucial component in microbial nitrogen cycling in both natural and engineered systems. Under specific conditions, including transitions from anoxic to oxic conditions and/or excessive ammonia loading, and the presence of high nitrite (NO₂⁻) concentrations, these bacteria are also documented to produce nitric oxide (NO) and nitrous oxide (N₂O) gases. Essentially, ammonia oxidation in the presence of non-limiting substrate concentrations (ammonia and O₂) is associated with N₂O production. An exceptional scenario that leads to such conditions is the periodical switch between anoxic and oxic conditions, which is rather common in engineered nitrogen-removal systems. In particular, the recovery from, rather than imposition of, anoxic conditions has been demonstrated to result in N₂O production. However, applied engineering perspectives, so far, have largely ignored the contribution of nitrification to N₂O emissions in greenhouse gas inventories from wastewater-treatment plants. Recent field-scale measurements have revealed that nitrification-related N₂O emissions are generally far higher than emissions assigned to heterotrophic denitrification. In the present paper, the metabolic pathways, which could potentially contribute to NO and N₂O production by AOB have been conceptually reconstructed under conditions especially relevant to engineered nitrogen-removal systems. Taken together, the reconstructed pathways, field- and laboratory-scale results suggest that engineering designs that achieve low effluent aqueous nitrogen concentrations also minimize gaseous nitrogen emissions.

Immobilization of metal wastes by reaction with H2S in anoxic basins: concept and elaboration.

PubMed

Schuiling, R D

2013-10-01

Metal wastes are produced in large quantities by a number of industries. Their disposal in isolated waste deposits is certain to cause many subsequent problems, because every material will sooner or later return to the geochemical cycle. The sealing of disposal sites usually starts to leak, often within a short time after the disposal site has been filled. The contained heavy metals are leached from the waste deposit and will contaminate the soil and the groundwater. It is evident that storage as metal sulfides in a permanently anoxic environment is the only safe way to handle metal wastes. The world's largest anoxic basin, the Black Sea, can serve as a georeactor. The metal wastes are sustainably transformed into harmless and immobile solids. These are incorporated in the lifeless bottom muds, where they are stored for millions of years.

Mimicking microbial interactions under nitrate-reducing conditions in an anoxic bioreactor: enrichment of novel Nitrospirae bacteria distantly related to Thermodesulfovibrio.

PubMed

Arshad, Arslan; Dalcin Martins, Paula; Frank, Jeroen; Jetten, Mike S M; Op den Camp, Huub J M; Welte, Cornelia U

2017-12-01

Microorganisms are main drivers of the sulfur, nitrogen and carbon biogeochemical cycles. These elemental cycles are interconnected by the activity of different guilds in sediments or wastewater treatment systems. Here, we investigated a nitrate-reducing microbial community in a laboratory-scale bioreactor model that closely mimicked estuary or brackish sediment conditions. The bioreactor simultaneously consumed sulfide, methane and ammonium at the expense of nitrate. Ammonium oxidation occurred solely by the activity of anammox bacteria identified as Candidatus Scalindua brodae and Ca. Kuenenia stuttgartiensis. Fifty-three percent of methane oxidation was catalyzed by archaea affiliated to Ca. Methanoperedens and 47% by Ca. Methylomirabilis bacteria. Sulfide oxidation was mainly shared between two proteobacterial groups. Interestingly, competition for nitrate did not lead to exclusion of one particular group. Metagenomic analysis showed that the most abundant taxonomic group was distantly related to Thermodesulfovibrio sp. (87-89% 16S rRNA gene identity, 52-54% average amino acid identity), representing a new family within the Nitrospirae phylum. A high quality draft genome of the new species was recovered, and analysis showed high metabolic versatility. Related microbial groups are found in diverse environments with sulfur, nitrogen and methane cycling, indicating that these novel Nitrospirae bacteria might contribute to biogeochemical cycling in natural habitats. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Sulfur during the Transition from Anoxic to Oxic Atmospheres

NASA Technical Reports Server (NTRS)

Zahnle, Kevin; Catling, David; Claire, Mark

2006-01-01

The invention of oxygenic photosynthesis was likely accompanied by the introduction of large amounts of O2 and complementary reduced gases (chiefly CH4) into the atmosphere. To first approximation the venting of O2 and CH4 are stochiometrically linked. We therefore present a suite of numerical photochemical models that address the anoxic-oxic transition in an atmosphere driven by large linked inputs of biogenic 02 and CH4. We find in general that, in steady state, there are two solutions, one oxic and the other anoxic. The anoxic solution appears to be linearly stable. If volcanic SO2 fluxes are large, S disproportionates into oxidized (H2S04) and reduced (S8) exit channels. As elemental sulfur is insoluble it provides a means of preserving photochemical mass-independent fractionation (MIF). On the other hand, if the source of volcanic SO2 is smaller than today, all S can leave the atmosphere as S8. Under these conditions there would be no MIF signal. The oxic solution appears to be linearly unstable. In the oxic solutions S is invariably oxidized to sulfate, and the MIF signal would be absent. The transitional atmosphere is relatively unstable and is also the most photochemically active. Consequently it is the transitional atmosphere, not the oxic or anoxic atmospheres, that has the lowest CH4 levels and weakest greenhouse warming. As a practical matter we expect the transitional atmospheres to vary strongly in response to diurnal and seasonal biological forcing.

Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions

PubMed Central

Angel, Roey; Claus, Peter; Conrad, Ralf

2012-01-01

The prototypical representatives of the Euryarchaeota—the methanogens—are oxygen sensitive and are thought to occur only in highly reduced, anoxic environments. However, we found methanogens of the genera Methanosarcina and Methanocella to be present in many types of upland soils (including dryland soils) sampled globally. These methanogens could be readily activated by incubating the soils as slurry under anoxic conditions, as seen by rapid methane production within a few weeks, without any additional carbon source. Analysis of the archaeal 16S ribosomal RNA gene community profile in the incubated samples through terminal restriction fragment length polymorphism and quantification through quantitative PCR indicated dominance of Methanosarcina, whose gene copy numbers also correlated with methane production rates. Analysis of the δ13C of the methane further supported this, as the dominant methanogenic pathway was in most cases aceticlastic, which Methanocella cannot perform. Sequences of the key methanogenic enzyme methyl coenzyme M reductase retrieved from the soil samples before incubation confirmed that Methanosarcina and Methanocella are the dominant methanogens, though some sequences of Methanobrevibacter and Methanobacterium were also detected. The global occurrence of only two active methanogenic archaea supports the hypothesis that these are autochthonous members of the upland soil biome and are well adapted to their environment. PMID:22071343

Distribution and Diversity of Symbiotic Thermophiles, Symbiobacterium thermophilum and Related Bacteria, in Natural Environments

PubMed Central

Ueda, Kenji; Ohno, Michiyo; Yamamoto, Kaori; Nara, Hanae; Mori, Yujiro; Shimada, Masafumi; Hayashi, Masahiko; Oida, Hanako; Terashima, Yuko; Nagata, Mitsuyo; Beppu, Teruhiko

2001-01-01

Symbiobacterium thermophilum is a tryptophanase-positive thermophile which shows normal growth only in coculture with its supporting bacteria. Analysis of the 16S rRNA gene (rDNA) indicated that the bacterium belongs to a novel phylogenetic branch at the outermost position of the gram-positive bacterial group without clustering to any other known genus. Here we describe the distribution and diversity of S. thermophilum and related bacteria in the environment. Thermostable tryptophanase activity and amplification of the specific 16S rDNA fragment were effectively employed to detect the presence of Symbiobacterium. Enrichment with kanamycin raised detection sensitivity. Mixed cultures of thermophiles containing Symbiobacterium species were frequently obtained from compost, soil, animal feces, and contents in the intestinal tracts, as well as feeds. Phylogenetic analysis and denaturing gradient gel electrophoresis of the specific 16S rDNA amplicons revealed a diversity of this group of bacteria in the environment. PMID:11525967

Integrated multi-omics analyses reveal the biochemical mechanisms and phylogenetic relevance of anaerobic androgen biodegradation in the environment

PubMed Central

Yang, Fu-Chun; Chen, Yi-Lung; Tang, Sen-Lin; Yu, Chang-Ping; Wang, Po-Hsiang; Ismail, Wael; Wang, Chia-Hsiang; Ding, Jiun-Yan; Yang, Cheng-Yu; Yang, Chia-Ying; Chiang, Yin-Ru

2016-01-01

Steroid hormones, such as androgens, are common surface-water contaminants. However, literature on the ecophysiological relevance of steroid-degrading organisms in the environment, particularly in anoxic ecosystems, is extremely limited. We previously reported that Steroidobacter denitrificans anaerobically degrades androgens through the 2,3-seco pathway. In this study, the genome of Sdo. denitrificans was completely sequenced. Transcriptomic data revealed gene clusters that were distinctly expressed during anaerobic growth on testosterone. We isolated and characterized the bifunctional 1-testosterone hydratase/dehydrogenase, which is essential for anaerobic degradation of steroid A-ring. Because of apparent substrate preference of this molybdoenzyme, corresponding genes, along with the signature metabolites of the 2,3-seco pathway, were used as biomarkers to investigate androgen biodegradation in the largest sewage treatment plant in Taipei, Taiwan. Androgen metabolite analysis indicated that denitrifying bacteria in anoxic sewage use the 2,3-seco pathway to degrade androgens. Metagenomic analysis and PCR-based functional assays showed androgen degradation in anoxic sewage by Thauera spp. through the action of 1-testosterone hydratase/dehydrogenase. Our integrative ‘omics' approach can be used for culture-independent investigations of the microbial degradation of structurally complex compounds where isotope-labeled substrates are not easily available. PMID:26872041

Open Questions on the Origin of Life at Anoxic Geothermal Fields

PubMed Central

Mulkidjanian, Armen Y.; Bychkov, Andrew Yu.; Dibrova, Daria V.; Galperin, Michael Y.; Koonin, Eugene V.

2014-01-01

We have recently reconstructed the ‘hatcheries’ of the first cells by combining geochemical analysis with phylogenomic scrutiny of the inorganic ion requirements of universal components of modern cells (Mulkidjanian et al.: Origin of first cells at terrestrial, anoxic geothermal fields. Proc Natl Acad Sci USA 2012, 109:E821–830). These ubiquitous, and by inference primordial, proteins and functional systems show affinity to and functional requirement for K+, Zn2+, Mn2+, and phosphate. Thus, protocells must have evolved in habitats with a high K+/Na+ ratio and relatively high concentrations of Zn, Mn and phosphorous compounds. Geochemical reconstruction shows that the ionic composition conducive to the origin of cells could not have existed in marine settings but is compatible with emissions of vapor-dominated zones of inland geothermal systems. Under anoxic, CO2-dominated atmosphere, the ionic composition of pools of cool, condensed vapor at anoxic geothermal fields would resemble the internal milieu of modern cells. Such pools would be lined with porous silicate minerals mixed with metal sulfides and enriched in K+ ions and phosphorous compounds. Here we address some questions that have appeared in print after the publication of our anoxic geothermal field scenario. We argue that anoxic geothermal fields, which were identified as likely cradles of life by using a top-down approach and phylogenomics analysis as a tool, could provide geochemical conditions similar to those which were suggested as most conducive for the emergence of life by the chemists who pursuit the complementary bottom-up strategy. PMID:23132762

Model photoautrophs isolated from a Proterozoic ocean analog - aerobic life under anoxic conditions

NASA Astrophysics Data System (ADS)

Hamilton, T. L.; de Beer, D.; Klatt, J.; Macalady, J.; Weber, M.; Lott, C.; Chennu, A.

2016-12-01

The 1-2 billion year delay before the final rise of oxygen at the end of the Proterozoic represents an important gap in our understanding of ancient biogeochemical cycling. Primary production fueled by sulfide-dependent anoxygenic photosynthesis, including the activity of metabolically versatile cyanobacteria, has been invoked as a mechanism for sustaining low atmospheric O2 throughout much of the Proterozoic. However, we understand very little about photoautotrophs that inhabit Proterozoic-like environments present on Earth today. Here we report on the isolation and characterization of a cyanobacterium and a green sulfur bacterium that are the dominant members of pinnacle mats in Little Salt Spring—a karst sinkhole in Florida with perennially low levels of dissolved oxygen and sulfide. The red pinnacle mats bloom in the anoxic basin of the sinkhole and receive light that is of very poor quality to support photosynthesis. Characterization of the isolates is consistent with observations of oxygenic and anoxygenic photosynthesis in situ—both organisms perform anoxygenic photosynthesis under conditions of very low light quality and quantity. Oxygenic photosynthesis by the cyanobacterium isolate is inhibited by the presence of sulfide and under optimal light conditions, rates of anoxygenic photosynthesis are nearly double that of oxygenic photosynthesis. The green sulfur bacterium is tolerant of oxygen and has a very low affinity for sulfide. In Little Salt Spring, oxygenic photosynthesis occurs for only four hours a day and the water column remains anoxic because of a continuous supply of sulfide. Isolation and characterization of these photoautotrophs combined with our high resolution microsensor data in situ highlight microbial biogeochemical cycling in this exceptional site where aerobic microorganisms persist in a largely anoxic ecosystem.

Hydrobiogeochemical interactions in 'anoxic' limestone drains for neutralization of acidic mine drainage

USGS Publications Warehouse

Robbins, E.I.; Cravotta, C.A.; Savela, C.E.; Nord, G.L.

1999-01-01

Processes affecting neutralization of acidic coal mine drainage were evaluated within 'anoxic' limestone drains (ALDs). Influents had pH???3.5 and dissolved oxygen <2 mg/l. Even though effluents were near neutral (pH 6 and alkalinity acidity), two of the four ALDs were failing due to clogging. Mineral-saturation indices indicated the potential for dissolution of calcite and gypsum, and precipitation of Al3+ and Fe3+ compounds. Cleavage mounts of calcite and gypsum that were suspended within the ALDs and later examined microscopically showed dissolution features despite coatings by numerous bacteria, biofilms, and Fe-Al-Si precipitates. In the drain exhibiting the greatest flow reduction, Al-hydroxysulfates had accumulated on limestone surfaces and calcite etch points, thus causing the decline in transmissivity and dissolution. Therefore, where Al loadings are high and flow rates are low, a pre-treatment step is indicated to promote Al removal before diverting acidic mine water into alkalinity-producing materials. ?? 1998 Elsevier Science Ltd.

Single-cell genomics reveals co-metabolic interactions within uncultivated Marine Group A bacteria

NASA Astrophysics Data System (ADS)

Hawley, A. K.; Hallam, S. J.

2016-02-01

Marine Group A (MGA) bacteria represent a ubiquitous and abundant candidate phylum enriched in oxygen minimum zones (OMZs) and the deep ocean. Despite MGA prevalence little is known about their ecology and biogeochemistry. Here we chart the metabolic potential of 26 MGA single-cell amplified genomes sourced from different environments spanning ecothermodynamic gradients including open ocean waters, OMZs and methanogenic environments including a terephthalate-degrading bioreactor. Metagenomic contig recruitment to SAGs combined with tetra-nucleotide frequency distribution patterns resolved nine MGA population genome bins. All population genomes exhibited genomic streamlining with open ocean MGA being the most reduced. Different strategies for carbohydrate utilization, carbon fixation energy metabolism and respiratory pathways were identified between population genome bins, including various roles in the nitrogen and sulfur cycles. MGA inhabiting OMZ oxyclines encoded genes for partial denitrification with potential to feed into anammox and nitrification as well as a polysulfide reductase with a potential role in the cryptic sulfur cycle. MGA inhabiting anoxic waters, encoded NiFe hydrogenase and nitrous oxide reductase with the potential to complete partial denitrification pathways previously linked to sulfur oxidation in SUP05 bacteria. MGA from methanogenic environments encoded genes mediating cascading syntrophic interactions with fatty acid degraders and methanogens including reverse electron transport potential. The MGA phylum appears to have evolved alternative metabolic innovations adapting specific subgroups to occupy specific niches along ecothermodynamic gradients. Additionally, expression of MGA genes from different OMZ environments supports that these subgroups manifest an increasing propensity for co-metabolic interactions under energy limiting conditions that mandates a cooperative mode of existence with important implications for C, N and S cycling in

New data concerning the geochemistry of unconsolidated sediments collected from the anoxic zone of the Black Sea

NASA Astrophysics Data System (ADS)

Duliu, Octavian G.; Cristache, Carmen; Florea, Nelida; Oaie, Gheorghe; Culicov, Otilia A.; Frontasyeva, Marina V.

2010-05-01

The content of eight major, rock forming elements (Na, Cl, Al, Si, K, Ca, Ti, Fe) and 34 trace elements (B, S, Sc, V, Cr, Mn, Co, Ni, Zn, As, Se, Br, Rb, Sr, Zr, Mo, Sn, Sb, Cs, Ba, La, Ce, Nd, Sm, Eu, Gd, Tb, Dy, Yb, Hf, Ta, W, Th and U) were determined by Prompt Gamma and Epithermal Neutron Activation Analysis in 45 samples of the uppermost 50 cm of undisturbed sediments collected from an anoxic continental zone of the Black Sea at a depth of 600 m, off the City of Constanta. 137Cs geochronology has evidenced a sedimentation ratio of 0,42 ± 0,12 mm/y which, by extrapolation to the entire 50 cm column gave an age of 1300 ± 300 y for the oldest sediments. Principal Component Analysis (PCA), Sc-La-Th and Co-Hf-Th ternary diagrams as well as La/Th ratio were used to interpret these data in correlation with the corresponding ones for the Upper Continental Crust (UCC), North American Shale Composite (NASC), as well as Atlantic, Pacific and Indian MORBs. At the same time the Se/Al, Se/Sc, Se/Mn, Mo/Al, Mo/Sc and Mo/Mn, ratios were used as indicators for anoxic conditions along sedimentary core. Major components distribution showed, that excepting CaO, their contents are very close to UCC and NASC, while the Principal Component Analysis evidenced three clusters consisting of Na, K and Cl, Al, Ti and Fe and respectively Ca, in concordance with the sediments' mineralogical composition. The Trace Elements Distribution was also close to UCC except for redox sensitive metals Se and Mo whose contents were 10 to 100 times higher than the corresponding UCC ones, this fact reflecting the anoxic conditions along the entire column of sediments. Moreover, by using Se and Mo as proxies for an anoxic environment, we estimated a relative consistency of the local conditions for a period between 350 ± 60 and 1300 ± 300 BP followed by a more fluctuant one during the last 300 years, this peculiarity also being confirmed by PCA, as well as by the vertical distribution of La/Th ratio. A

Abundant Trimethylornithine Lipids and Specific Gene Sequences Are Indicative of Planctomycete Importance at the Oxic/Anoxic Interface in Sphagnum-Dominated Northern Wetlands.

PubMed

Moore, Eli K; Villanueva, Laura; Hopmans, Ellen C; Rijpstra, W Irene C; Mets, Anchelique; Dedysh, Svetlana N; Sinninghe Damsté, Jaap S

2015-09-01

Northern wetlands make up a substantial terrestrial carbon sink and are often dominated by decay-resistant Sphagnum mosses. Recent studies have shown that planctomycetes appear to be involved in degradation of Sphagnum-derived debris. Novel trimethylornithine (TMO) lipids have recently been characterized as abundant lipids in various Sphagnum wetland planctomycete isolates, but their occurrence in the environment has not yet been confirmed. We applied a combined intact polar lipid (IPL) and molecular analysis of peat cores collected from two northern wetlands (Saxnäs Mosse [Sweden] and Obukhovskoye [Russia]) in order to investigate the preferred niche and abundance of TMO-producing planctomycetes. TMOs were present throughout the profiles of Sphagnum bogs, but their concentration peaked at the oxic/anoxic interface, which coincided with a maximum abundance of planctomycete-specific 16S rRNA gene sequences. The sequences detected at the oxic/anoxic interface were affiliated with the Isosphaera group, while sequences present in the anoxic peat layers were related to an uncultured planctomycete group. Pyrosequencing-based analysis identified Planctomycetes as the major bacterial group at the oxic/anoxic interface at the Obukhovskoye peat (54% of total 16S rRNA gene sequence reads), followed by Acidobacteria (19% reads), while in the Saxnäs Mosse peat, Acidobacteria were dominant (46%), and Planctomycetes contributed to 6% of the total reads. The detection of abundant TMO lipids in planctomycetes isolated from peat bogs and the lack of TMO production by cultures of acidobacteria suggest that planctomycetes are the producers of TMOs in peat bogs. The higher accumulation of TMOs at the oxic/anoxic interface and the change in the planctomycete community with depth suggest that these IPLs could be synthesized as a response to changing redox conditions at the oxic/anoxic interface. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Abundant Trimethylornithine Lipids and Specific Gene Sequences Are Indicative of Planctomycete Importance at the Oxic/Anoxic Interface in Sphagnum-Dominated Northern Wetlands

PubMed Central

Villanueva, Laura; Hopmans, Ellen C.; Rijpstra, W. Irene C.; Mets, Anchelique; Dedysh, Svetlana N.

2015-01-01

Northern wetlands make up a substantial terrestrial carbon sink and are often dominated by decay-resistant Sphagnum mosses. Recent studies have shown that planctomycetes appear to be involved in degradation of Sphagnum-derived debris. Novel trimethylornithine (TMO) lipids have recently been characterized as abundant lipids in various Sphagnum wetland planctomycete isolates, but their occurrence in the environment has not yet been confirmed. We applied a combined intact polar lipid (IPL) and molecular analysis of peat cores collected from two northern wetlands (Saxnäs Mosse [Sweden] and Obukhovskoye [Russia]) in order to investigate the preferred niche and abundance of TMO-producing planctomycetes. TMOs were present throughout the profiles of Sphagnum bogs, but their concentration peaked at the oxic/anoxic interface, which coincided with a maximum abundance of planctomycete-specific 16S rRNA gene sequences. The sequences detected at the oxic/anoxic interface were affiliated with the Isosphaera group, while sequences present in the anoxic peat layers were related to an uncultured planctomycete group. Pyrosequencing-based analysis identified Planctomycetes as the major bacterial group at the oxic/anoxic interface at the Obukhovskoye peat (54% of total 16S rRNA gene sequence reads), followed by Acidobacteria (19% reads), while in the Saxnäs Mosse peat, Acidobacteria were dominant (46%), and Planctomycetes contributed to 6% of the total reads. The detection of abundant TMO lipids in planctomycetes isolated from peat bogs and the lack of TMO production by cultures of acidobacteria suggest that planctomycetes are the producers of TMOs in peat bogs. The higher accumulation of TMOs at the oxic/anoxic interface and the change in the planctomycete community with depth suggest that these IPLs could be synthesized as a response to changing redox conditions at the oxic/anoxic interface. PMID:26150465

Oxygen Delivery from Hyperbarically Loaded Microtanks Extends Cell Viability in Anoxic Environments

PubMed Central

Cook, Colin A.; Hahn, Kathryn C.; Morrissette-McAlmon, Justin B.F.; Grayson, Warren L.

2016-01-01

Oxygen diffusion limitations within nascent tissue engineered (TE) grafts lead to the development of hypoxic regions, cell death, and graft failure. Previous efforts have been made to deliver oxygen within TE scaffolds, including peroxide-doping, perfluorocarbons, and hyperbaric oxygen therapy, to mitigate these effects and help maintain post transplantation cell viability, but these have suffered from significant drawbacks. Here we present a novel approach utilizing polymeric hollow-core microspheres that can be hyperbarically loaded with oxygen and subsequently provide prolonged oxygen delivery. These oxygen carriers are termed, microtanks. With an interest in orthopedic applications, we combined microtanks within polycaprolactone to form solid phase constructs with oxygen delivery capabilities. The mathematical laws governing oxygen delivery from microtank-loaded constructs are developed along with empirical validation. Constructs achieved periods of oxygen delivery out to 6 days, which was shown to prolong the survival of human adipose derived stem cells (hASCs) and human umbilical vein endothelial cells (HUVECs) as well as to enhance their cellular morphology under anoxic conditions. The results of this study suggest the microtank approach may be a feasible means of maintaining cell viability in TE scaffolds during the critical period of vascularization in vivo. PMID:25818444

A NON-STEADY-STATE DIAGENETIC MODEL FOR CHANGES IN SEDIMENT BIOGEOCHEMISTRY IN RESPONSE TO SEASONALLY HYPOXIC/ANOXIC CONDITIONS BENEATH THE MISSISSIPPI RIVER PLUME

EPA Science Inventory

Although the bottom waters of many freshwater and marine environments are either permanently oxic or anoxic, there is a growing appreciation that in many bodies of water near-bottom conditions seasonally oscillate between these extreme. Although observational databases for these ...

Distribution of multi-resistant Gram-negative versus Gram-positive bacteria in the hospital inanimate environment.

PubMed

Lemmen, S W; Häfner, H; Zolldann, D; Stanzel, S; Lütticken, R

2004-03-01

We prospectively studied the difference in detection rates of multi-resistant Gram-positive and multi-resistant Gram-negative bacteria in the inanimate environment of patients harbouring these organisms. Up to 20 different locations around 190 patients were surveyed. Fifty-four patients were infected or colonized with methicillin-resistant Staphylococcus aureus (MRSA) or vancomycin-resistant enterococci (VRE) and 136 with multi-resistant Gram-negative bacteria. The environmental detection rate for MRSA or VRE was 24.7% (174/705 samples) compared with 4.9% (89/1827 samples) for multi-resistant Gram-negative bacteria (P<0.001). Gram-positive bacteria were isolated more frequently than Gram-negatives from the hands of patients (P<0.001) and hospital personnel (P=0.1145). Environmental contamination did not differ between the intensive care units (ICUs) and the general wards (GWs), which is noteworthy because our ICUs are routinely disinfected twice a day, whereas GWs are cleaned just once a day with detergent. Current guidelines for the prevention of spread of multi-resistant bacteria in the hospital setting do not distinguish between Gram-positive and Gram-negative isolates. Our results suggest that the inanimate environment serves as a secondary source for MRSA and VRE, but less so for Gram-negative bacteria. Thus, strict contact isolation in a single room with complete barrier precautions is recommended for MRSA or VRE; however, for multi-resistant Gram-negative bacteria, contact isolation with barrier precautions for close contact but without a single room seems sufficient. This benefits not only the patients, but also the hospital by removing some of the strain placed on already over-stretched resources.

Airborne Bacteria in an Urban Environment

PubMed Central

Mancinelli, Rocco L.; Shulls, Wells A.

1978-01-01

Samples were taken at random intervals over a 2-year period from urban air and tested for viable bacteria. The number of bacteria in each sample was determined, and each organism isolated was identified by its morphological and biochemical characteristics. The number of bacteria found ranged from 0.013 to 1.88 organisms per liter of air sampled. Representatives of 19 different genera were found in 21 samples. The most frequently isolated organisms and their percent of occurence were Micrococcus (41%), Staphylococcus (11%), and Aerococcus (8%). The bacteria isolated were correlated with various weather and air pollution parameters using the Pearson product-moment correlation coefficient method. Statistically significant correlations were found between the number of viable bacteria isolated and the concentrations of nitric oxide (−0.45), nitrogen dioxide (+0.43), and suspended particulate pollutants (+0.56). Calculated individually, the total number of Micrococcus, Aerococcus, and Staphylococcus, number of rods, and number of cocci isolated showed negative correlations with nitric oxide and positive correlations with nitrogen dioxide and particulates. Statistically significant positive correlations were found between the total number of rods isolated and the concentration of nitrogen dioxide (+0.54) and the percent relative humidity (+0.43). The other parameters tested, sulfur dioxide, hydrocarbons, and temperature, showed no significant correlations. Images PMID:677875

First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea.

PubMed

Antunes, André; Alam, Intikhab; Simões, Marta Filipa; Daniels, Camille; Ferreira, Ari J S; Siam, Rania; El-Dorry, Hamza; Bajic, Vladimir B

2015-10-01

The deep-sea brines of the Red Sea include some of the most extreme and unique environments on Earth. They combine high salinities with increases in temperature, heavy metals, hydrostatic pressure, and anoxic conditions, creating unique settings for thriving populations of novel extremophiles. Despite a recent increase of studies focusing on these unusual biotopes, their viral communities remain unexplored. The current survey explores four metagenomic datasets obtained from different brine-seawater interface samples, focusing specifically on the diversity of their viral communities. Data analysis confirmed that the particle-attached viral communities present in the brine-seawater interfaces were diverse and generally dominated by Caudovirales, yet appearing distinct from sample to sample. With a level of caution, we report the unexpected finding of Phycodnaviridae, which infects algae and plants, and trace amounts of insect-infecting Iridoviridae. Results from Kebrit Deep revealed stratification in the viral communities present in the interface: the upper-interface was enriched with viruses associated with typical marine bacteria, while the lower-interface was enriched with haloviruses and halophages. These results provide first insights into the unexplored viral communities present in deep-sea brines of the Red Sea, representing one of the first steps for ongoing and future sampling efforts and studies. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

A Combination of Stable Isotope Probing, Illumina Sequencing, and Co-occurrence Network to Investigate Thermophilic Acetate- and Lactate-Utilizing Bacteria.

PubMed

Sun, Weimin; Krumins, Valdis; Dong, Yiran; Gao, Pin; Ma, Chunyan; Hu, Min; Li, Baoqin; Xia, Bingqing; He, Zijun; Xiong, Shangling

2018-01-01

Anaerobic digestion is a complicated microbiological process that involves a wide diversity of microorganisms. Acetate is one of the most important intermediates, and interactions between acetate-oxidizing bacteria and archaea could play an important role in the formation of methane in anoxic environments. Anaerobic digestion at thermophilic temperatures is known to increase methane production, but the effects on the microbial community are largely unknown. In the current study, stable isotope probing was used to characterize acetate- and lactate-oxidizing bacteria in thermophilic anaerobic digestion. In microcosms fed 13 C-acetate, bacteria related to members of Clostridium, Hydrogenophaga, Fervidobacterium, Spirochaeta, Limnohabitans, and Rhodococcus demonstrated elevated abundances of 13 C-DNA fractions, suggesting their activities in acetate oxidation. In the treatments fed 13 C-lactate, Anaeromyxobacter, Desulfobulbus, Syntrophus, Cystobacterineae, and Azospira were found to be the potential thermophilic lactate utilizers. PICRUSt predicted that enzymes related to nitrate and nitrite reduction would be enriched in 13 C-DNA fractions, suggesting that the acetate and lactate oxidation may be coupled with nitrate and/or nitrite reduction. Co-occurrence network analysis indicated bacterial taxa not enriched in 13 C-DNA fractions that may also play a critical role in thermophilic anaerobic digestion.

SAR11 bacteria linked to ocean anoxia and nitrogen loss

PubMed Central

Tsementzi, Despina; Wu, Jieying; Deutsch, Samuel; Nath, Sangeeta; Rodriguez-R, Luis M; Burns, Andrew S.; Ranjan, Piyush; Sarode, Neha; Malmstrom, Rex R.; Padilla, Cory C.; Stone, Benjamin K.; Bristow, Laura A.; Larsen, Morten; Glass, Jennifer B.; Thamdrup, Bo; Woyke, Tanja; Konstantinidis, Konstantinos T.; Stewart, Frank J.

2016-01-01

Summary Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. DNA sequences from SAR11 are also abundant in oxygen minimum zones (OMZs) where oxygen falls below detection and anaerobic microbes play important roles in converting bioavailable nitrogen to N2 gas. Evidence for anaerobic metabolism in SAR11 has not yet been observed, and the question of how these bacteria contribute to OMZ biogeochemical cycling is unanswered. Here, we identify the metabolic basis for SAR11 activity in anoxic ocean waters. Genomic analysis of single cells from the world’s largest OMZ revealed diverse and previously uncharacterized SAR11 lineages that peak in abundance at anoxic depths, but are largely undetectable in oxygen-rich ocean regions. OMZ SAR11 contain adaptations to low oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalyzing the nitrite-producing first step of denitrification and constituted ~40% of all OMZ nar transcripts, with transcription peaking in the zone of maximum nitrate reduction rates. These results redefine the ecological niche of Earth’s most abundant organismal group and suggest an important contribution of SAR11 to nitrite production in OMZs, and thus to pathways of ocean nitrogen loss. PMID:27487207

Development and application of kinetic model on biological anoxic/aerobic filter.

PubMed

Kim, Youngnoh; Tanaka, Kazuhiro; Lee, Yong-Woo; Chung, Jinwook

2008-01-01

An up-flow biological anoxic filter (BANF) has been developed to achieve high removal performance of suspended solids and BOD removal as well as nitrogen. With a view to understand treatment mechanisms, we developed a filtration model that incorporates filtration, deposit scoring and biological reactions simultaneously. The biological reactions consist of four types of reaction; dissolution of organic particles; utilization of dissolved organic matter; denitrification; and self-degradation of bacteria. Whereas the reactor is generally assumed to be a plug flow reactor in the filtration model, it is assumed a continuous-flow stirred tank reactor (CSTR) in the model of biological reactions. The hydrodynamics is supposed that the filter bottom (the portion sludge settled) is a CSTR and the filter bed (the portion filled with filter media) consists of number of CSTR of equal size arranged in series. The model obtained in this study was verified and simulated using experimental results taken from a pilot-scale plant and predicted the experimental data well, applying to design and operate BANF.

[Diversity of culturable sulfur-oxidizing bacteria in deep-sea hydrothermal vent environments of the South Atlantic].

PubMed

Xu, Hongxiu; Jiang, Lijing; Li, Shaoneng; Zhong, Tianhua; Lai, Qiliang; Shao, Zongze

2016-01-04

To investigate the diversity of culturable sulfur-oxidizing bacteria in hydrothermal vent environments of the South Atlantic, and analyze their characteristics of sulfur oxidation. We enriched and isolated sulfur-oxidizing bacteria from hydrothermal vent samples collected from the South Atlantic. The microbial diversity in enrichment cultures was analyzed using the Denatural Gradient Gel Electrophoresis method. Sulfur-oxidizing characteristics of the isolates was further studied by using ion chromatography. A total of 48 isolates were obtained from the deep-sea hydrothermal vent samples, which belonged to 23 genera and mainly grouped into alpha-Proteobacteria (58.3%), Actinobacteria (22.9%) and gama-Proteobacteria (18.8%). Among them, the genus Thalassospira, Martelella and Microbacterium were dominant. About 60% of the isolates exibited sulfur-oxidizing ability and strain L6M1-5 had a higher sulfur oxidation rate by comparison analysis. The diversity of sulfur-oxidizing bacteria in hydrothermal environments of the South Atlantic was reported for the first time based on culture-dependent methods. The result will help understand the biogechemical process of sulfur compounds in the deep-sea hydrothermal environments.

Fate of antibiotic resistant cultivable heterotrophic bacteria and antibiotic resistance genes in wastewater treatment processes.

PubMed

Zhang, Songhe; Han, Bing; Gu, Ju; Wang, Chao; Wang, Peifang; Ma, Yanyan; Cao, Jiashun; He, Zhenli

2015-09-01

Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are emerging contaminants of environmental concern. Heterotrophic bacteria in activated sludge have an important role in wastewater treatment plants (WWTPs). However, the fate of cultivable heterotrophic ARB and ARGs in WWPTs process remains unclear. In the present study, we investigated the antibiotic-resistant phenotypes of cultivable heterotrophic bacteria from influent and effluent water of three WWTPs and analysed thirteen ARGs in ARB and in activated sludge from anoxic, anaerobic and aerobic compartments. From each influent or effluent sample of the three plants, 200 isolates were randomly tested for susceptibility to 12 antibiotics. In these samples, between 5% and 64% isolates showed resistance to >9 antibiotics and the proportion of >9-drug-resistant bacteria was lower in isolates from effluent than from influent. Eighteen genera were identified in 188 isolates from influent (n=94) and effluent (n=94) of one WWTP. Six genera (Aeromonas, Bacillus, Lysinibacillus, Microbacterium, Providencia, and Staphylococcus) were detected in both influent and effluent samples. Gram-negative and -positive isolates dominated in influent and effluent, respectively. The 13 tetracycline-, sulphonamide-, streptomycin- and β-lactam-resistance genes were detected at a higher frequency in ARB from influent than from effluent, except for sulA and CTX-M, while in general, the abundances of ARGs in activated sludge from two of the three plants were higher in aerobic compartments than in anoxic ones, indicating abundant ARGs exit in the excess sledges and/or in uncultivable bacteria. These findings may be useful for elucidating the effect of WWTP on ARB and ARGs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Activation of DOR attenuates anoxic K+ derangement via inhibition of Na+ entry in mouse cortex.

PubMed

Chao, Dongman; Bazzy-Asaad, Alia; Balboni, Gianfranco; Salvadori, Severo; Xia, Ying

2008-09-01

We have recently found that in the mouse cortex, activation of delta-opioid receptor (DOR) attenuates the disruption of K(+) homeostasis induced by hypoxia or oxygen-glucose deprivation. This novel observation suggests that DOR may protect neurons from hypoxic/ischemic insults via the regulation of K(+) homeostasis because the disruption of K(+) homeostasis plays a critical role in neuronal injury under hypoxic/ischemic stress. The present study was performed to explore the ionic mechanism underlying the DOR-induced neuroprotection. Because anoxia causes Na(+) influx and thus stimulates K(+) leakage, we investigated whether DOR protects the cortex from anoxic K(+) derangement by targeting the Na(+)-based K(+) leakage. By using K(+)-sensitive microelectrodes in mouse cortical slices, we showed that 1) lowering Na(+) concentration and substituting with impermeable N-methyl-D-glucamine caused a concentration-dependent attenuation of anoxic K(+) derangement; 2) lowering Na(+) concentration by substituting with permeable Li(+) tended to potentiate the anoxic K(+) derangement; and 3) the DOR-induced protection against the anoxic K(+) responses was largely abolished by low-Na(+) perfusion irrespective of the substituted cation. We conclude that external Na(+) concentration greatly influences anoxic K(+) derangement and that DOR activation likely attenuates anoxic K(+) derangement induced by the Na(+)-activated mechanisms in the cortex.

Transport and removal of viruses in saturated sand columns under oxic and anoxic conditions--Potential implications for groundwater protection.

PubMed

Frohnert, Anne; Apelt, Susann; Klitzke, Sondra; Chorus, Ingrid; Szewzyk, Regine; Selinka, Hans-Christoph

2014-11-01

To protect groundwater as a drinking water resource from microbiological contamination, protection zones are installed. While travelling through these zones, concentrations of potential pathogens should decline to levels that pose no risks to human health. Removal of viruses during subsurface passage is influenced by physicochemical conditions, such as oxygen concentration, which also affects virus survival. The aim of our study was to evaluate the effect of redox conditions on the removal of viruses during sand filtration. Experiments in glass columns filled with medium-grained sand were conducted to investigate virus removal in the presence and absence of dissolved oxygen. Bacteriophages MS2 and PhiX174, as surrogates for human enteric viruses were spiked in pulsed or in continuous mode and pumped through the columns at a filter velocity of about 1m/d. Virus breakthrough curves were analyzed by calculating total viral elimination and fitted using one-dimensional transport models (CXTFIT and HYDRUS-1D). While short-term experiments with pulsed virus application showed only small differences with regard to virus removal under oxic and anoxic conditions, a long-term experiment with continuous dosing revealed a clearly lower elimination of viruses under anoxic conditions. These findings suggest that less inactivation and less adsorption of viruses in anoxic environments affect their removal. Therefore, in risk assessment studies aimed to secure drinking water resources from viral contamination and optimization of protection zones, the oxic and anoxic conditions in the subsurface should also be considered. Copyright © 2014 Elsevier GmbH. All rights reserved.

Growth of Carnobacterium spp. from permafrost under low pressure, temperature, and anoxic atmosphere has implications for Earth microbes on Mars.

PubMed

Nicholson, Wayne L; Krivushin, Kirill; Gilichinsky, David; Schuerger, Andrew C

2013-01-08

The ability of terrestrial microorganisms to grow in the near-surface environment of Mars is of importance to the search for life and protection of that planet from forward contamination by human and robotic exploration. Because most water on present-day Mars is frozen in the regolith, permafrosts are considered to be terrestrial analogs of the martian subsurface environment. Six bacterial isolates were obtained from a permafrost borehole in northeastern Siberia capable of growth under conditions of low temperature (0 °C), low pressure (7 mbar), and a CO(2)-enriched anoxic atmosphere. By 16S ribosomal DNA analysis, all six permafrost isolates were identified as species of the genus Carnobacterium, most closely related to C. inhibens (five isolates) and C. viridans (one isolate). Quantitative growth assays demonstrated that the six permafrost isolates, as well as nine type species of Carnobacterium (C. alterfunditum, C. divergens, C. funditum, C. gallinarum, C. inhibens, C. maltaromaticum, C. mobile, C. pleistocenium, and C. viridans) were all capable of growth under cold, low-pressure, anoxic conditions, thus extending the low-pressure extreme at which life can function.

Anoxic monimolimnia: Nutrients devious feeders or bombs ready to explode?

NASA Astrophysics Data System (ADS)

Gianni, Areti; Zacharias, Ierotheos

2015-04-01

Coastal regions are under strong human influence and its environmental impact is reflected into their water quality. Oligotrophic estuaries and coastal systems have changed in mesotrophic and/or eutrophic, shown an increase in toxic algal blooms, hypoxic/anoxic events, and massive mortalities of many aquatic and benthic organisms. In strongly stratified and productive water basins, bottom water dissolved oxygen is depleted due to the excessive organic matter decomposition in these depths. Distribution and recycling of nutrients in their water column is inextricably dependent on oxygenation and redox conditions. Bottom water anoxia accelerates PO43-, NH4+ and H2S recycling and accumulation from organic matter decomposition. The anoxic, H2S, PO43- and NH4+ rich bottom water constitutes a toxic layer, threatening the balance of the entire ecosystem. In permanently stratified water basins, storm events could result in stratification destruction and water column total mixing. The turnover brings large amounts of H2S to the surface resulting in low levels of oxygen and massive fish kills. PO43- and NH4+ are released to the interface and surface waters promoting algal blooms. Μore organic matter is produced fueling anoxia. The arising question is, whether the balance of an anoxic water ecosystem is under the threat of its hypolimnetic nutrient and sulfide load, only in the case of storm events and water column total mixing. In polymictic water basins it is clear that the accumulated, in the bottom layer, nutrients will supply surface waters, after the pycnocline overturn. Besides this mechanism of basins' water quality degradation is nowadays recognized as one of the biggest obstacles in eutrophic environments management and restoration efforts. The role of internal load, in permanently stratified water basins, is not so clear. In the present study the impact of storm events on water column stability and bottom water anoxia of meromictic coastal basins, is investigated

Microbial Formation of Dimethyl Sulfide in Anoxic Sphagnum Peat

PubMed Central

Kiene, R. P.; Hines, M. E.

1995-01-01

Peat bogs dominated by Sphagnum spp. have relatively high areal rates of dimethyl sulfide (DMS) emission to the atmosphere. DMS was produced in anoxic slurries of Sphagnum peat with a linear time course and with an average rate of 40.4 (range, 22.0 to 68.6) nmol per liter of slurry (middot) day(sup-1) observed in nine batches of slurry. Methanethiol (MeSH) was produced at roughly similar rates over the typical 4- to 8-day incubations. DMS and MeSH production in these acidic (pH 4.2 to 4.6) peats were biological, as they were stopped completely by autoclaving and inhibited strongly by addition of antibiotics and 500 (mu)M chloroform. Endogenous DMS production may be due to the degradation of S-methyl-methionine, dimethyl sulfoxide, or methoxyaromatic compounds (e.g., syringic acid), each of which stimulated DMS formation when added at 5 to 10 (mu)M concentrations. However, on the basis of the high rates of thiol (MeSH and ethanethiol) methylation activity that we observed and the availability of endogenous MeSH, we suggest that methylation of MeSH is the major pathway leading to DMS formation in anaerobic peat. Solid-phase adsorption of MeSH plays a key role in its availability for biomethylation reactions. Additions of acetate (1.5 mM) or compounds which could cause acetate to accumulate (e.g., glucose, alanine, and 2-bromoethanesulfonate) suppressed DMS formation. It is likely that acetogenic bacteria are involved in DMS formation, but our data are insufficient to allow firm conclusions about the metabolic pathways or organisms involved. Our observations are the first which point to the methylation of MeSH as the major mechanism for endogenous DMS production in any environment. The rates of net DMS production observed are sufficient to explain the relatively high fluxes of DMS emitted to the atmosphere from Sphagnum sp.-dominated wetlands. PMID:16535080

Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reeve, Wayne

2013-03-01

Wayne Reeve of Murdoch University on "Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

Stabilization of waste-activated sludge through the anoxic-aerobic digestion process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hashimoto, S.; Fujita, M.; Terai, K.

1982-08-01

During the aerobic digestion process, the nitrogen which had been embedded in the activated sludge is solubilized to form ammoniacal and nitric nitrogen which are in turn transferred to the liquor and cause the increase of nitrogen loading in the sewage treatment plant. In this study, the anoxic-aerobic sludge digestion system which is a modified form of the conventional aerobic sludge digestion is made up of aerobic and anoxic tanks and are designed to remove both the volatile suspended solids and the total nitrogen (TN) simultaneously. The removal efficiencies of both VSS and TN were investigated by feeding waste-activated sludgemore » continuously and semicontinuously. The maximum percent reduction of both VSS and TN was achieved at a Q /SUB r/ /Q /SUB s/ ratio of 2 in the continuous process. The semicontinuous process was used to improve the nitrogen removal efficiency further. In the semicontinuous process, the VSS reduction efficiency as well as the nitrogen removal efficiency increased remarkably under a constant Q /SUB r/ /Q /SUB s/ ratio of 2. This process also achieved a VSS reduction efficiency higher than the aerobic digestion process (control). It was suggested that the additional anoxic tank enhanced the sludge digestion. Furthermore, the anoxic-aerobic digestion system can be applied to other treatment media like the primary sludge, industrial sludge, animal manure, etc.« less

Stabilization of waste-activated sludge through the anoxic-aerobic digestion process.

PubMed

Hashimoto, S; Fujita, M; Terai, K

1982-08-01

During the aerobic digestion process, the nitrogen which had been embedded in the activated sludge is solubilized to form ammoniacal and nitric nitrogen which are in turn transferred to the liquor and cause the increase of nitrogen loading in the sewage treatment plant. In this study, the anoxic-aerobic sludge digestion system which is a modified form of the conventional aerobic sludge digestion is made up of aerobic and anoxic tanks and are designed to remove both the volatile suspended solids and the total nitrogen (TN) simultaneously. The removal efficiencies of both VSS and TN were investigated by feeding waste-activated sludge continuously and semicontinuously. The maximum percent reduction of both VSS and TN was achieved at a Q(r)/Q(s) ratio of 2 in the continuous process. The semicontinuous process was used to improve the nitrogen removal efficiency further. In the semicontinuous process, the VSS reduction efficiency as well as the nitrogen removal efficiency increased remarkably under a constant Q(r)/Q(s) ratio of 2. This process also achieved a VSS reduction efficiency higher than the aerobic digestion process (control). It was suggested that the additional anoxic tank enhanced the sludge digestion. Furthermore, the anoxic-aerobic digestion system can be applied to other treatment media like the primary sludge, industrial sludge, animal manure, etc.

NC10 bacteria in marine oxygen minimum zones

PubMed Central

Padilla, Cory C; Bristow, Laura A; Sarode, Neha; Garcia-Robledo, Emilio; Gómez Ramírez, Eddy; Benson, Catherine R; Bourbonnais, Annie; Altabet, Mark A; Girguis, Peter R; Thamdrup, Bo; Stewart, Frank J

2016-01-01

Bacteria of the NC10 phylum link anaerobic methane oxidation to nitrite denitrification through a unique O2-producing intra-aerobic methanotrophy pathway. A niche for NC10 in the pelagic ocean has not been confirmed. We show that NC10 bacteria are present and transcriptionally active in oceanic oxygen minimum zones (OMZs) off northern Mexico and Costa Rica. NC10 16S rRNA genes were detected at all sites, peaking in abundance in the anoxic zone with elevated nitrite and methane concentrations. Phylogenetic analysis of particulate methane monooxygenase genes further confirmed the presence of NC10. rRNA and mRNA transcripts assignable to NC10 peaked within the OMZ and included genes of the putative nitrite-dependent intra-aerobic pathway, with high representation of transcripts containing the unique motif structure of the nitric oxide (NO) reductase of NC10 bacteria, hypothesized to participate in O2-producing NO dismutation. These findings confirm pelagic OMZs as a niche for NC10, suggesting a role for this group in OMZ nitrogen, methane and oxygen cycling. PMID:26918666

Metabolic and transcriptional regulatory mechanisms underlying the anoxic adaptation of rice coleoptile

PubMed Central

Lakshmanan, Meiyappan; Mohanty, Bijayalaxmi; Lim, Sun-Hyung; Ha, Sun-Hwa; Lee, Dong-Yup

2014-01-01

The ability of rice to germinate under anoxia by extending the coleoptile is a highly unusual characteristic and a key feature underpinning the ability of rice seeds to establish in such a stressful environment. The process has been a focal point for research for many years. However, the molecular mechanisms underlying the anoxic growth of the coleoptile still remain largely unknown. To unravel the key regulatory mechanisms of rice germination under anoxic stress, we combined in silico modelling with gene expression data analysis. Our initial modelling analysis via random flux sampling revealed numerous changes in rice primary metabolism in the absence of oxygen. In particular, several reactions associated with sucrose metabolism and fermentation showed a significant increase in flux levels, whereas reaction fluxes across oxidative phosphorylation, the tricarboxylic acid cycle and the pentose phosphate pathway were down-regulated. The subsequent comparative analysis of the differences in calculated fluxes with previously published gene expression data under air and anoxia identified at least 37 reactions from rice central metabolism that are transcriptionally regulated. Additionally, cis-regulatory content analyses of these transcriptionally controlled enzymes indicate a regulatory role for transcription factors such as MYB, bZIP, ERF and ZnF in transcriptional control of genes that are up-regulated during rice germination and coleoptile elongation under anoxia. PMID:24894389

SAR11 bacteria linked to ocean anoxia and nitrogen loss

NASA Astrophysics Data System (ADS)

Tsementzi, Despina; Wu, Jieying; Deutsch, Samuel; Nath, Sangeeta; Rodriguez-R, Luis M.; Burns, Andrew S.; Ranjan, Piyush; Sarode, Neha; Malmstrom, Rex R.; Padilla, Cory C.; Stone, Benjamin K.; Bristow, Laura A.; Larsen, Morten; Glass, Jennifer B.; Thamdrup, Bo; Woyke, Tanja; Konstantinidis, Konstantinos T.; Stewart, Frank J.

2016-08-01

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here, genomic analysis of single cells from the world’s largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. These results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth’s most abundant organismal group.

SAR11 bacteria linked to ocean anoxia and nitrogen loss.

PubMed

Tsementzi, Despina; Wu, Jieying; Deutsch, Samuel; Nath, Sangeeta; Rodriguez-R, Luis M; Burns, Andrew S; Ranjan, Piyush; Sarode, Neha; Malmstrom, Rex R; Padilla, Cory C; Stone, Benjamin K; Bristow, Laura A; Larsen, Morten; Glass, Jennifer B; Thamdrup, Bo; Woyke, Tanja; Konstantinidis, Konstantinos T; Stewart, Frank J

2016-08-11

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here, genomic analysis of single cells from the world's largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. These results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth's most abundant organismal group.

Increased thermohaline stratification as a possible cause for an ocean anoxic event in the Cretaceous period.

PubMed

Erbacher, J; Huber, B T; Norris, R D; Markey, M

2001-01-18

Ocean anoxic events were periods of high carbon burial that led to drawdown of atmospheric carbon dioxide, lowering of bottom-water oxygen concentrations and, in many cases, significant biological extinction. Most ocean anoxic events are thought to be caused by high productivity and export of carbon from surface waters which is then preserved in organic-rich sediments, known as black shales. But the factors that triggered some of these events remain uncertain. Here we present stable isotope data from a mid-Cretaceous ocean anoxic event that occurred 112 Myr ago, and that point to increased thermohaline stratification as the probable cause. Ocean anoxic event 1b is associated with an increase in surface-water temperatures and runoff that led to decreased bottom-water formation and elevated carbon burial in the restricted basins of the western Tethys and North Atlantic. This event is in many ways similar to that which led to the more recent Plio-Pleistocene Mediterranean sapropels, but the greater geographical extent and longer duration (approximately 46 kyr) of ocean anoxic event 1b suggest that processes leading to such ocean anoxic events in the North Atlantic and western Tethys were able to act over a much larger region, and sequester far more carbon, than any of the Quaternary sapropels.

Degradation of trifluoroacetate in oxic and anoxic sediments

USGS Publications Warehouse

Visscher, P.T.; Culbertson, C.W.; Oremland, R.S.

1994-01-01

THE deleterious effect of chlorofluorocarbons on stratospheric ozone has led to international cooperation to end their use. The search for acceptable alternatives has focused on hydrofluorocarbons (HFCs) or hydrochlorofluorocarbons (HCFCs) which are attractive because they have relatively short atmospheric residence times. HFCs and HCFCs are attacked by tropospheric hydroxyl radicals, leading to the formation of trifluoroacetate (TFA). Most of the atmospheric TFA is deposited at the Earth's surface, where it is thought to be highly resistant to bacterial attack. Therefore, use of HCFCs and HFCs may lead to accumulation of TFA in soils, where it could prove toxic or inhibitory to plants and soil microbial communities. Although little is known about the toxicity of TFA, monofluoroacetate, which occurs at low levels in some plants and which is susceptible to slow attack by aerobic soil microbes, is known to be acutely toxic. Here we report that TFA can be rapidly degraded microbially under anoxic and oxic conditions. These results imply that significant microbial sinks exist in nature for the elimination of TFA from the environment. We also show that oxic degradation of TFA leads to the formation of fluoroform, a potential ozone-depleting compound with a much longer atmospheric lifetime than the parent compounds.The deleterious effect of chlorofluorcarbons on stratospheric ozone has led to international cooperation to end their use. The search for acceptable alternatives has focused on hydroflnorocarbons (HFCs) or hydrochloroflnorcarbons (HCFs) which are attractive because they have relatively short atmospheric residence times. HFCs and HCFs are attacked by tropospheric hydroxyl radicals, leading to the formation of trifluoroacetate (TFA). Most of the atmospheric TFA is deposited at the Earth's surface, where it is thought to be highly resistant to bacterial attack. Therefore, use of HCFs and HCFs may lead to accummulation of TFA in soils, where it could prove toxic

Molecular Detection of Anaerobic Ammonium-Oxidizing (Anammox) Bacteria in High-Temperature Petroleum Reservoirs

PubMed Central

Li, Hui; Chen, Shuo; Mu, Bo-Zhong

2010-01-01

Anaerobic ammonium-oxidizing (anammox) process plays an important role in the nitrogen cycle of the worldwide anoxic and mesophilic habitats. Recently, the existence and activity of anammox bacteria have been detected in some thermophilic environments, but their existence in the geothermal subterranean oil reservoirs is still not reported. This study investigated the abundance, distribution and functional diversity of anammox bacteria in nine out of 17 high-temperature oil reservoirs by molecular ecology analysis. High concentration (5.31–39.2 mg l−1) of ammonium was detected in the production water from these oilfields with temperatures between 55°C and 75°C. Both 16S rRNA and hzo molecular biomarkers indicated the occurrence of anammox bacteria in nine out of 17 samples. Most of 16S rRNA gene phylotypes are closely related to the known anammox bacterial genera Candidatus Brocadia, Candidatus Kuenenia, Candidatus Scalindua, and Candidatus Jettenia, while hzo gene phylotypes are closely related to the genera Candidatus Anammoxoglobus, Candidatus Kuenenia, Candidatus Scalindua, and Candidatus Jettenia. The total bacterial and anammox bacterial densities were 6.4 ± 0.5 × 103 to 2.0 ± 0.18 × 106 cells ml−1 and 6.6 ± 0.51 × 102 to 4.9 ± 0.36 × 104 cell ml−1, respectively. The cluster I of 16S rRNA gene sequences showed distant identity (<92%) to the known Candidatus Scalindua species, inferring this cluster of anammox bacteria to be a new species, and a tentative name Candidatus “Scalindua sinooilfield” was proposed. The results extended the existence of anammox bacteria to the high-temperature oil reservoirs. PMID:20740282

Molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in high-temperature petroleum reservoirs.

PubMed

Li, Hui; Chen, Shuo; Mu, Bo-Zhong; Gu, Ji-Dong

2010-11-01

Anaerobic ammonium-oxidizing (anammox) process plays an important role in the nitrogen cycle of the worldwide anoxic and mesophilic habitats. Recently, the existence and activity of anammox bacteria have been detected in some thermophilic environments, but their existence in the geothermal subterranean oil reservoirs is still not reported. This study investigated the abundance, distribution and functional diversity of anammox bacteria in nine out of 17 high-temperature oil reservoirs by molecular ecology analysis. High concentration (5.31-39.2 mg l(-1)) of ammonium was detected in the production water from these oilfields with temperatures between 55°C and 75°C. Both 16S rRNA and hzo molecular biomarkers indicated the occurrence of anammox bacteria in nine out of 17 samples. Most of 16S rRNA gene phylotypes are closely related to the known anammox bacterial genera Candidatus Brocadia, Candidatus Kuenenia, Candidatus Scalindua, and Candidatus Jettenia, while hzo gene phylotypes are closely related to the genera Candidatus Anammoxoglobus, Candidatus Kuenenia, Candidatus Scalindua, and Candidatus Jettenia. The total bacterial and anammox bacterial densities were 6.4 ± 0.5 × 10(3) to 2.0 ± 0.18 × 10(6) cells ml(-1) and 6.6 ± 0.51 × 10(2) to 4.9 ± 0.36 × 10(4) cell ml(-1), respectively. The cluster I of 16S rRNA gene sequences showed distant identity (<92%) to the known Candidatus Scalindua species, inferring this cluster of anammox bacteria to be a new species, and a tentative name Candidatus "Scalindua sinooilfield" was proposed. The results extended the existence of anammox bacteria to the high-temperature oil reservoirs.

Mathematical modeling of nitrous oxide production in an anaerobic/oxic/anoxic process.

PubMed

Ding, Xiaoqian; Zhao, Jianqiang; Hu, Bo; Chen, Ying; Ge, Guanghuan; Li, Xiaoling; Wang, Sha; Gao, Kun; Tian, Xiaolei

2016-12-01

This study incorporates three currently known nitrous oxide (N 2 O) production pathways: ammonium-oxidizing bacteria (AOB) denitrification, incomplete hydroxylamine (NH 2 OH) oxidation, and heterotrophic denitrification on intracellular polymers, into a mathematical model to describe N 2 O production in an anaerobic/oxic/anoxic (AOA) process for the first time. The developed model was calibrated and validated by four experimental cases, then evaluated by two independent anaerobic/aerobic (AO) studies from literature. The modeling results displayed good agreement with the measured data. N 2 O was primarily generated in the aerobic stage by AOB denitrification (67.84-81.64%) in the AOA system. Smaller amounts of N 2 O were produced via incomplete NH 2 OH oxidation (15.61-32.17%) and heterotrophic denitrification on intracellular polymers (0-12.47%). The high nitrite inhibition on N 2 O reductase led to the increased N 2 O accumulation in heterotrophic denitrification on intracellular polymers. The new model was capable of modeling nitrification-denitrification dynamics and heterotrophic denitrification on intracellular polymers in the AOA system. Copyright © 2016 Elsevier Ltd. All rights reserved.

Quantification and identification of particle-associated bacteria in unchlorinated drinking water from three treatment plants by cultivation-independent methods.

PubMed

Liu, G; Ling, F Q; Magic-Knezev, A; Liu, W T; Verberk, J Q J C; Van Dijk, J C

2013-06-15

Water quality regulations commonly place quantitative limits on the number of organisms (e.g., heterotrophic plate count and coliforms) without considering the presence of multiple cells per particle, which is only counted as one regardless how many cells attached. Therefore, it is important to quantify particle-associated bacteria (PAB), especially cells per particle. In addition, PAB may house (opportunistic) pathogens and have higher resistance to disinfection than planktonic bacteria. It is essential to know bacterial distribution on particles. However, limited information is available on quantification and identification of PAB in drinking water. In the present study, PAB were sampled from the unchlorinated drinking water at three treatment plants in the Netherlands, each with different particle compositions. Adenosine triphosphate (ATP) and total cell counts (TCC) with flow cytometry were used to quantify the PAB, and high-throughput pyrosequencing was used to identify them. The number and activity of PAB ranged from 1.0 to 3.5 × 10(3) cells ml(-1) and 0.04-0.154 ng l(-1) ATP. There were between 25 and 50 cells found to be attached on a single particle. ATP per cell in PAB was higher than in planktonic bacteria. Among the identified sequences, Proteobacteria were found to be the most dominant phylum at all locations, followed by OP3 candidate division and Nitrospirae. Sequences related to anoxic bacteria from the OP3 candidate division and other anaerobic bacteria were detected. Genera of bacteria were found appear to be consistent with the major element composition of the associated particles. The presence of multiple cells per particle challenges the use of quantitative methods such as HPC and Coliforms that are used in the current drinking water quality regulations. The detection of anoxic and anaerobic bacteria suggests the ecological importance of PAB in drinking water distribution systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

Isolation and characterization of bacteria capable of tolerating the extreme conditions of clean room environments.

PubMed

La Duc, Myron T; Dekas, Anne; Osman, Shariff; Moissl, Christine; Newcombe, David; Venkateswaran, Kasthuri

2007-04-01

In assessing the bacterial populations present in spacecraft assembly, spacecraft test, and launch preparation facilities, extremophilic bacteria (requiring severe conditions for growth) and extremotolerant bacteria (tolerant to extreme conditions) were isolated. Several cultivation approaches were employed to select for and identify bacteria that not only survive the nutrient-limiting conditions of clean room environments but can also withstand even more inhospitable environmental stresses. Due to their proximity to spacefaring objects, these bacteria pose a considerable risk for forward contamination of extraterrestrial sites. Samples collected from four geographically distinct National Aeronautics and Space Administration clean rooms were challenged with UV-C irradiation, 5% hydrogen peroxide, heat shock, pH extremes (pH 3.0 and 11.0), temperature extremes (4 degrees C to 65 degrees C), and hypersalinity (25% NaCl) prior to and/or during cultivation as a means of selecting for extremotolerant bacteria. Culture-independent approaches were employed to measure viable microbial (ATP-based) and total bacterial (quantitative PCR-based) burdens. Intracellular ATP concentrations suggested a viable microbial presence ranging from below detection limits to 10(6) cells/m(2). However, only 0.1 to 55% of these viable cells were able to grow on defined culture medium. Isolated members of the Bacillaceae family were more physiologically diverse than those reported in previous studies, including thermophiles (Geobacillus), obligate anaerobes (Paenibacillus), and halotolerant, alkalophilic species (Oceanobacillus and Exiguobacterium). Non-spore-forming microbes (alpha- and beta-proteobacteria and actinobacteria) exhibiting tolerance to the selected stresses were also encountered. The multiassay cultivation approach employed herein enhances the current understanding of the physiological diversity of bacteria housed in these clean rooms and leads us to ponder the origin and means

Arsenite and Ferrous Iron Oxidation Linked to Chemolithotrophic Denitrification for the Immobilization of Arsenic in Anoxic Environments

PubMed Central

Sun, Wenjie; Sierra-Alvarez, Reyes; Milner, Lily; Oremland, Ron; Field, Jim A.

2014-01-01

The objective of this study was to explore a bioremediation strategy based on injecting NO3− to support the anoxic oxidation of ferrous iron (Fe(II)) and arsenite (As(III)) in the subsurface as a means to immobilize As in the form of arsenate (As(V)) adsorbed onto biogenic ferric (Fe(III)) (hydr)oxides. Continuous flow sand filled columns were used to simulate a natural anaerobic groundwater and sediment system with co-occurring As(III) and Fe(II) in the presence (SF1) or absence (SF2) of nitrate, respectively. During operation for 250 days, the average influent arsenic concentration of 567 µg l−1 was reduced to 10.6 (±9.6) µg l−1 in the effluent of column SF1. The cumulative removal of Fe(II) and As(III) in SF1 was 6.5–10-fold higher than that in SF2. Extraction and measurement of the mass of iron and arsenic immobilized on the sand packing of the columns was close to the iron and arsenic removed from the aqueous phase during column operation. The dominant speciation of the immobilized iron and arsenic was Fe(III) and As(V) in SF1, compared with Fe(II) and As(III) in SF2. The speciation was confirmed by XRD and XPS. The results indicate that microbial oxidation of As(III) and Fe(II) linked to denitrification resulted in the enhanced immobilization of aqueous arsenic in anaerobic environments by forming Fe(III) (hydr)oxides coated sands with adsorbed As(V). PMID:19764221

Reflex anoxic seizures ('white breath-holding'): nonepileptic vagal attacks.

PubMed Central

Stephenson, J B

1978-01-01

From clinical history 58 children were diagnosed as having reflex anoxic seizures secondary to provoked cardioinhibition (also known as white breath-holding attacks). Before referral, these seizures were commonly misdiagnosed as epileptic either because the provocation was ignored, not recognised, or was a febrile illness, or because there was no crying, no obvious breath-holding, little cyanosis, and often no pallor to suggest syncope and cerebral ischaemia. The duration of cardiac asystole after ocular compression was measured in these children and in 60 additional children with other paroxysmal disorders. In 45 (78%) of the 58 with reflex anoxic seizures asystole was 2 seconds or over, and in 32 (55%) it was 4 seconds or greater, an abnormal response. Review of the literature supports the concept that these seizures result from vagal-mediated reflex cardiac arrest which can if necessary be prevented by atropine. The simple name 'vagal attack' is proposed. Ocular compression under EEG and ECG control supports the clinical diagnosis if asystole and/or an anoxic seizure is induced; the procedure described is safe and should be routine in seizure or syncope evaluation, when a meticulous history still leaves room for doubt. Images Figs. 1-8 p194-b p194-c p194-d p194-e p194-f p194-g p194-h PMID:348123

Isolation of iron bacteria from terrestrial and aquatic environments

NASA Astrophysics Data System (ADS)

Schmidt, Bertram; Szewzyk, Ulrich

2010-05-01

Bacteria, which are capable of iron oxidation or at least iron deposition are widely distributed in environments where zones of dissolved ferrous iron and oxygen gradients are overlapping [1]. They take part in the biological cycling of iron and influence other cycles of elements for example carbon [2]. Manganese can be used for similar metabolic purposes as iron, because it can be biologically oxidized by chemolithotrophs or can be reduced by respirating bacteria as well [3, 4]. Bacterial activity is responsible for the accumulation of ferric iron compounds in their surroundings. The formation of bog ore is a well known example for a soil horizon, with an extreme enrichment of biogenic ferric iron [5]. We focused on the isolation of neutrophilic iron bacteria and bacteria capable of manganese oxidation. We used samples from Tierra del Fuego (Argentina) the National Park "Unteres Odertal" (Germany) and Berlin ground water wells. Microscopic examination of the samples revealed a considerable diversity of iron encrusted structures of bacterial origin. Most of these morphologic types are already well known. The taxonomic classification of many of these organisms is based on morphologic features and is not reliable compared to recent methods of molecular biology. That is mainly due to the fact, that most of these bacteria are hardly culturable or do not show their characteristic morphologic features under culture conditions. We established a collection of more than 300 iron depositing strains. Phylogenetic analyses showed that we have many yet uncultured strains in pure culture. We obtained many isolates which form distinct branches within long known iron bacteria groups like the Sphaerotilus-Leptothrix cluster. But some of the strains belong to groups, which have not yet been associated with iron oxidation activity. The strains deposit high amounts of oxidized iron and manganese compounds under laboratory conditions. However it is unclear if these precipitations are

Sludge reduction and microbial community structure in an anaerobic/anoxic/oxic process coupled with potassium ferrate disintegration.

PubMed

An, Ying; Zhou, Zhen; Yao, Jie; Niu, Tianhao; Qiu, Zhan; Ruan, Danian; Wei, Haijuan

2017-12-01

An anaerobic/anoxic/oxic (AAO) wastewater treatment system combining with a potassium ferrate (K 2 FeO 4 ) oxidation side-stream reactor (SSR) was proposed for sludge reduction. Batch experiments showed that optimal K 2 FeO 4 dosage and reaction time for sludge disintegration was 100mg/g suspended solids (SS) and 24h, respectively. Subsequently, an AAO-SSR and a conventional AAO were operated in parallel to investigate effects of K 2 FeO 4 oxidation on process performance, sludge characteristics and microbial community structures. The AAO-SSR process operated under the optimized condition achieved efficient COD and NH 4 + -N removal, and reduced sludge by 47.5% with observed yield coefficient of 0.21gSS/g COD. K 2 FeO 4 addition broke sludge particles, increased dissolved organic matters in the mixed liquor, and improved sludge dewaterability. Illumina-MiSeq sequencing results showed that K 2 FeO 4 oxidation in the AAO-SSR decreased microbial richness and diversity, enriched slow growers (Dechloromonas), anaerobic fermentative bacteria (Azospira) and Fe(III)-reducing bacteria (Ferribacterium), but limited the growth of phosphate-accumulating organisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

Treatment of synthetic refinery wastewater in anoxic-aerobic sequential moving bed reactors and sulphur recovery.

PubMed

Mallick, Subrat Kumar; Chakraborty, Saswati

2017-11-10

Objective of the present study was to simultaneously biodegrade synthetic petroleum refinery wastewater containing phenol (750 mg/L), sulphide (750 mg/L), hydrocarbon (as emulsified diesel of 300 mg/L), ammonia-nitrogen (350 mg/L) at pH >9 in anoxic-aerobic sequential moving bed reactors. The optimum mixing speed of anoxic reactor was observed at 20 rpm and beyond that, removal rate remained constant. In anoxic reactor the minimum hydraulic retention time was observed to be 2 days for complete removal of sulphide, 40-50% removal of phenol and total hydrocarbons and 52% of sulphur recovery. The optimum HRT of aerobic moving bed reactor was observed as 16 h (total HRT of 64 h for anoxic and aerobic reactors) for complete removals of phenol, total hydrocarbons, COD (chemical oxygen demand) and ammonia-nitrogen with nitrification.

Growth of Carnobacterium spp. from permafrost under low pressure, temperature, and anoxic atmosphere has implications for Earth microbes on Mars

PubMed Central

Nicholson, Wayne L.; Krivushin, Kirill; Gilichinsky, David; Schuerger, Andrew C.

2013-01-01

The ability of terrestrial microorganisms to grow in the near-surface environment of Mars is of importance to the search for life and protection of that planet from forward contamination by human and robotic exploration. Because most water on present-day Mars is frozen in the regolith, permafrosts are considered to be terrestrial analogs of the martian subsurface environment. Six bacterial isolates were obtained from a permafrost borehole in northeastern Siberia capable of growth under conditions of low temperature (0 °C), low pressure (7 mbar), and a CO2-enriched anoxic atmosphere. By 16S ribosomal DNA analysis, all six permafrost isolates were identified as species of the genus Carnobacterium, most closely related to C. inhibens (five isolates) and C. viridans (one isolate). Quantitative growth assays demonstrated that the six permafrost isolates, as well as nine type species of Carnobacterium (C. alterfunditum, C. divergens, C. funditum, C. gallinarum, C. inhibens, C. maltaromaticum, C. mobile, C. pleistocenium, and C. viridans) were all capable of growth under cold, low-pressure, anoxic conditions, thus extending the low-pressure extreme at which life can function. PMID:23267097

Stimulated anoxic biodegradation of aromatic hydrocarbons using Fe(III) ligands

USGS Publications Warehouse

Lovley, D.R.; Woodward, J.C.; Chapelle, F.H.

1994-01-01

Contamination of ground waters with water-soluble aromatic hydrocarbons, common components of petroleum pollution, often produces anoxic conditions under which microbial degradation of the aromatics is slow. Oxygen is often added to contaminated ground water to stimulate biodegradation, but this can be technically difficult and expensive. Insoluble Fe(III) oxides, which are generally abundant in shallow aquifers, are alternative potential oxidants, but are difficult for microorganisms to access. Here we report that adding organic ligands that bind to Fe(III) dramatically increases its bioavailability, and that in the presence of these ligands, rates of degradation of aromatic hydrocarbons in anoxic aquifer sediments are comparable to those in oxic sediments. We find that even benzene, which is notoriously refractory in the absence of oxygen, can be rapidly degraded. Our results suggest that increasing the bioavailability of Fe(III) by adding suitable ligands provides a potential alternative to oxygen addition for the bioremediation of petroleum-contaminated aquifers.Contamination of ground waters with water-soluble aromatic hydrocarbons, common components of petroleum pollution, often produces anoxic conditions under which microbial degradation of the aromatics is slow. Oxygen is often added to contaminated ground water to stimulate biodegradation, but this can be technically difficult and expensive. Insoluble Fe(III) oxides, which are generally abundant in shallow aquifers, are alternative potential oxidants, but are difficult for microorganisms to access. Here we report that adding organic ligands that bind to Fe(III) dramatically increases its bioavailability, and that in the presence of these ligands, rates of degradation of aromatic hydrocarbons in anoxic aquifer sediments are comparable to those in oxic sediments. We find that even benzene, which is notoriously refractory in the absence of oxygen, can be rapidly degraded. Our results suggest that increasing

Testing the Role of Microbial Ecology, Redox-Mediated Deep Water Production and Hypersalinity on TEX86: Lipids and 16s Sequences from Archaea and Bacteria in the Water Column and Sediments of Orca Basin

NASA Astrophysics Data System (ADS)

Warren, C.; Romero, I.; Ellis, G.; Goddard, E.; Krishnan, S.; Nigro, L. M.; Super, J. R.; Zhang, Y.; Zhuang, G.; Hollander, D. J.; Pagani, M.

2014-12-01

Mesophilic marine archaea and bacteria are known to substantially contribute to the oceanic microbial biomass and play critical roles in global carbon, nitrogen and nutrient cycles. The Orca Basin, a 2400 meter deep bathymetric depression on the continental slope of the north-central Gulf of Mexico, is an ideal environment to examine how redox-dependent biochemical processes control the input and cycling of bacterial and archaea-derived lipid compounds from formation in near-surface water, through secondary recycling processes operating at the redox-transition in the water column, to sedimentary diagenetic processes operating in oxic to anoxic zones within the basin. The lowermost 180 meters of the Orca Basin is characterized by an anoxic, hypersaline brine that is separated from the overlying oxic seawater by a well-defined redox sequence associated with a systematic increasing in salinity from 35 - 250‰. While surface water conditions are viewed as normal marine with a seasonally productive water column, the sub-oxic to anoxic transition zones within the deep-water column and the sediment spans over 200 m allowing the unique opportunity for discrete sampling of resident organisms and lipids. Here we present 16s rRNA sequence data of Bacteria and Archaea collected parallel to GDGT lipid profiles and in situ environmental measurements from the sediment and overlying water column in the intermediate zone of the basin, where movements of chemical transition zones are preserved. We evaluated GDGTs and corresponding taxa across the surface water, chlorophyll maximum, thermocline, and the deep redox boundary, including oxygenation, denitrification, manganese, iron and sulfate reduction zones, to determine if GDGTs are being produced under these conditions and how surface-derived GDGT lipids and the TEX86 signal may be altered. The results have implications for the application of the TEX86 paleotemperature proxy.

Exploring the evolution of multicellularity in Saccharomyces cerevisiae under bacteria environment: An experimental phylogenetics approach.

PubMed

Quintero-Galvis, Julian F; Paleo-López, Rocío; Solano-Iguaran, Jaiber J; Poupin, María Josefina; Ledger, Thomas; Gaitan-Espitia, Juan Diego; Antoł, Andrzej; Travisano, Michael; Nespolo, Roberto F

2018-05-01

There have been over 25 independent unicellular to multicellular evolutionary transitions, which have been transformational in the complexity of life. All of these transitions likely occurred in communities numerically dominated by unicellular organisms, mostly bacteria. Hence, it is reasonable to expect that bacteria were involved in generating the ecological conditions that promoted the stability and proliferation of the first multicellular forms as protective units. In this study, we addressed this problem by analyzing the occurrence of multicellularity in an experimental phylogeny of yeasts ( Sacharomyces cerevisiae ) a model organism that is unicellular but can generate multicellular clusters under some conditions. We exposed a single ancestral population to periodic divergences, coevolving with a cocktail of environmental bacteria that were inoculated to the environment of the ancestor, and compared to a control (no bacteria). We quantified culturable microorganisms to the level of genera, finding up to 20 taxa (all bacteria) that competed with the yeasts during diversification. After 600 generations of coevolution, the yeasts produced two types of multicellular clusters: clonal and aggregative. Whereas clonal clusters were present in both treatments, aggregative clusters were only present under the bacteria treatment and showed significant phylogenetic signal. However, clonal clusters showed different properties if bacteria were present as follows: They were more abundant and significantly smaller than in the control. These results indicate that bacteria are important modulators of the occurrence of multicellularity, providing support to the idea that they generated the ecological conditions-promoting multicellularity.

Sulfate-reducing bacteria in rice field soil and on rice roots.

PubMed

Wind, T; Stubner, S; Conrad, R

1999-05-01

Rice plants that were grown in flooded rice soil microcosms were examined for their ability to exhibit sulfate reducing activity. Washed excised rice roots showed sulfate reduction potential when incubated in anaerobic medium indicating the presence of sulfate-reducing bacteria. Rice plants, that were incubated in a double-chamber (phylloshpere and rhizosphere separated), showed potential sulfate reduction rates in the anoxic rhizosphere compartment. These rates decreased when oxygen was allowed to penetrate through the aerenchyma system of the plants into the anoxic root compartment, indicating that sulfate reducers on the roots were partially inhibited by oxygen or that sulfate was regenerated by oxidation of reduced S-compounds. The potential activity of sulfate reducers on rice roots was consistent with MPN enumerations showing that H2-utilizing sulfate-reducing bacteria were present in high numbers on the rhizoplane (4.1 x 10(7) g-1 root fresh weight) and in the adjacent rhizosperic soil (2.5 x 10(7) g-1 soil dry weight). Acetate-oxidizing sulfate reducers, on the other hand, showed highest numbers in the unplanted bulk soil (1.9 x 10(6) g-1 soil dry weight). Two sulfate reducing bacteria were isolated from the highest dilutions of the MPN series and were characterized physiologically and phylogenetically. Strain F1-7b which was isolated from the rhizoplane with H2 as electron donor was related to subgroup II of the family Desulfovibrionaceae. Strain EZ-2C2, isolated from the rhizoplane on acetate, grouped together with Desulforhabdus sp. and Syntrophobacter wolinii. Other strains of sulfate-reducing bacteria originated from bulk soil of rice soil microcosms and were isolated using different electron donors. From these isolates, strains R-AcA1, R-IbutA1, R-PimA1 and R-AcetonA170 were Gram-positive bacteria which were affiliated with the genus Desulfotomaculum. The other isolates were members of subgroup II of the Desulfovibrionaceae (R-SucA1 and R-LacA1), were

Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments

PubMed Central

Khalsa-Moyers, Gurusahai; Alexandre, Gladys; Sukharnikov, Leonid O.; Wuichet, Kristin; Hurst, Gregory B.; McDonald, W. Hayes; Robertson, Jon S.; Barbe, Valérie; Calteau, Alexandra; Rouy, Zoé; Mangenot, Sophie; Prigent-Combaret, Claire; Normand, Philippe; Boyer, Mickaël; Siguier, Patricia; Dessaux, Yves; Elmerich, Claudine; Condemine, Guy; Krishnen, Ganisan; Kennedy, Ivan; Paterson, Andrew H.; González, Victor; Mavingui, Patrick; Zhulin, Igor B.

2011-01-01

Fossil records indicate that life appeared in marine environments ∼3.5 billion years ago (Gyr) and transitioned to terrestrial ecosystems nearly 2.5 Gyr. Sequence analysis suggests that “hydrobacteria” and “terrabacteria” might have diverged as early as 3 Gyr. Bacteria of the genus Azospirillum are associated with roots of terrestrial plants; however, virtually all their close relatives are aquatic. We obtained genome sequences of two Azospirillum species and analyzed their gene origins. While most Azospirillum house-keeping genes have orthologs in its close aquatic relatives, this lineage has obtained nearly half of its genome from terrestrial organisms. The majority of genes encoding functions critical for association with plants are among horizontally transferred genes. Our results show that transition of some aquatic bacteria to terrestrial habitats occurred much later than the suggested initial divergence of hydro- and terrabacterial clades. The birth of the genus Azospirillum approximately coincided with the emergence of vascular plants on land. PMID:22216014

Attenuation and colloidal mobilization of bacteriophages in natural sediments under anoxic as compared to oxic conditions.

PubMed

Klitzke, Sondra; Schroeder, Jendrik; Selinka, Hans-Christoph; Szewzyk, Regine; Chorus, Ingrid

2015-06-15

Redox conditions are known to affect the fate of viruses in porous media. Several studies report the relevance of colloid-facilitated virus transport in the subsurface, but detailed studies on the effect of anoxic conditions on virus retention in natural sediments are still missing. Therefore, we investigated the fate of viruses in natural flood plain sediments with different sesquioxide contents under anoxic conditions by considering sorption to the solid phase, sorption to mobilized colloids, and inactivation in the aqueous phase. Batch experiments were conducted under oxic and anoxic conditions at pH values between 5.1 and 7.6, using bacteriophages MS2 and PhiX174 as model viruses. In addition to free and colloid-associated bacteriophages, dissolved and colloidal concentrations of Fe, Al and organic C as well as dissolved Ca were determined. Results showed that regardless of redox conditions, bacteriophages did not adsorb to mobilized colloids, even under favourable charge conditions. Under anoxic conditions, attenuation of bacteriophages was dominated by sorption over inactivation, with MS2 showing a higher degree of sorption than PhiX174. Inactivation in water was low under anoxic conditions for both bacteriophages with about one log10 decrease in concentration during 16 h. Increased Fe/Al concentrations and a low organic carbon content of the sediment led to enhanced bacteriophage removal under anoxic conditions. However, even in the presence of sufficient Fe/A-(hydr)oxides on the solid phase, bacteriophage sorption was low. We presume that organic matter may limit the potential retention of sesquioxides in anoxic sediments and should thus be considered for the risk assessment of virus breakthrough in the subsurface. Copyright © 2015 Elsevier B.V. All rights reserved.

Unexpected and novel putative viruses in the sediments of a deep-dark permanently anoxic freshwater habitat

PubMed Central

Borrel, Guillaume; Colombet, Jonathan; Robin, Agnès; Lehours, Anne-Catherine; Prangishvili, David; Sime-Ngando, Télesphore

2012-01-01

Morphological diversity, abundance and community structure of viruses were examined in the deep and anoxic sediments of the volcanic Lake Pavin (France). The sediment core, encompassing 130 years of sedimentation, was subsampled every centimeter. High viral abundances were recorded and correlated to prokaryotic densities. Abundances of viruses and prokaryotes decreased with the depth, contrasting the pattern of virus-to-prokaryote ratio. According to fingerprint analyses, the community structure of viruses, bacteria and archaea gradually changed, and communities of the surface (0–10 cm) could be discriminated from those of the intermediate (11–27 cm) and deep (28–40 cm) sediment layers. Viral morphotypes similar to virions of ubiquitous dsDNA viruses of bacteria were observed. Exceptional morphotypes, previously never reported in freshwater systems, were also detected. Some of these resembled dsDNA viruses of hyperthermophilic and hyperhalophilic archaea. Moreover, unusual types of spherical and cubic virus-like particles (VLPs) were observed. Infected prokaryotic cells were detected in the whole sediment core, and their vertical distribution correlated with both viral and prokaryotic abundances. Pleomorphic ellipsoid VLPs were visible in filamentous cells tentatively identified as representatives of the archaeal genus Methanosaeta, a major group of methane producers on earth. PMID:22648129

Unexpected and novel putative viruses in the sediments of a deep-dark permanently anoxic freshwater habitat.

PubMed

Borrel, Guillaume; Colombet, Jonathan; Robin, Agnès; Lehours, Anne-Catherine; Prangishvili, David; Sime-Ngando, Télesphore

2012-11-01

Morphological diversity, abundance and community structure of viruses were examined in the deep and anoxic sediments of the volcanic Lake Pavin (France). The sediment core, encompassing 130 years of sedimentation, was subsampled every centimeter. High viral abundances were recorded and correlated to prokaryotic densities. Abundances of viruses and prokaryotes decreased with the depth, contrasting the pattern of virus-to-prokaryote ratio. According to fingerprint analyses, the community structure of viruses, bacteria and archaea gradually changed, and communities of the surface (0-10 cm) could be discriminated from those of the intermediate (11-27 cm) and deep (28-40 cm) sediment layers. Viral morphotypes similar to virions of ubiquitous dsDNA viruses of bacteria were observed. Exceptional morphotypes, previously never reported in freshwater systems, were also detected. Some of these resembled dsDNA viruses of hyperthermophilic and hyperhalophilic archaea. Moreover, unusual types of spherical and cubic virus-like particles (VLPs) were observed. Infected prokaryotic cells were detected in the whole sediment core, and their vertical distribution correlated with both viral and prokaryotic abundances. Pleomorphic ellipsoid VLPs were visible in filamentous cells tentatively identified as representatives of the archaeal genus Methanosaeta, a major group of methane producers on earth.

Reduction of ferric iron by acidophilic heterotrophic bacteria: evidence for constitutive and inducible enzyme systems in Acidiphilium spp.

PubMed

Johnson, D B; Bridge, T A M

2002-01-01

To compare the abilities of two obligately acidophilic heterotrophic bacteria, Acidiphilium acidophilum and Acidiphilium SJH, to reduce ferric iron to ferrous when grown under different culture conditions. Bacteria were grown in batch culture, under different aeration status, and in the presence of either ferrous or ferric iron. The specific rates of ferric iron reduction by fermenter-grown Acidiphilium SJH were unaffected by dissolved oxygen (DO) concentrations, while iron reduction by A. acidophilum was highly dependent on DO concentrations in the growth media. The ionic form of iron present (ferrous or ferric) had a minimal effect on the abilities of harvested cells to reduce ferric iron. Whole cell protein profiles of Acidiphilium SJH were very similar, regardless of the DO status of the growth medium, while additional proteins were present in A. acidophilum grown microaerobically compared with aerobically-grown cells. The dissimilatory reduction of ferric iron is constitutive in Acidiphilium SJH while it is inducible in A. acidophilum. Ferric iron reduction by Acidiphilium spp. may occur in oxygen-containing as well as anoxic acidic environments. This will detract from the effectiveness of bioremediation systems where removal of iron from polluted waters is mediated via oxidation and precipitation of the metal.

Nitrogen-removal performance and community structure of nitrifying bacteria under different aeration modes in an oxidation ditch.

PubMed

Guo, Chang-Zi; Fu, Wei; Chen, Xue-Mei; Peng, Dang-Cong; Jin, Peng-Kang

2013-07-01

Oxidation-ditch operation modes were simulated using sequencing batch reactors (SBRs) with alternate stirring and aerating. The nitrogen-removal efficiencies and nitrifying characteristics of two aeration modes, point aeration and step aeration, were investigated. Under the same air-supply capacity, oxygen dissolved more efficiently in the system with point aeration, forming a larger aerobic zone. The nitrifying effects were similar in point aeration and step aeration, where the average removal efficiencies of NH4(+) N were 98% and 96%, respectively. When the proportion of anoxic and oxic zones was 1, the average removal efficiencies of total nitrogen (TN) were 45% and 66% under point aeration and step aeration, respectively. Step aeration was more beneficial to both anoxic denitrification and simultaneous nitrification and denitrification (SND). The maximum specific ammonia-uptake rates (AUR) of point aeration and step aeration were 4.7 and 4.9 mg NH4(+)/(gMLVSS h), respectively, while the maximum specific nitrite-uptake rates (NUR) of the two systems were 7.4 and 5.3 mg NO2(-)-N/(gMLVSS h), respectively. The proportions of ammonia-oxidizing bacteria (AOB) to all bacteria were 5.1% under point aeration and 7.0% under step aeration, and the proportions of nitrite-oxidizing bacteria (NOB) reached 6.5% and 9.0% under point and step aeration, respectively. The dominant genera of AOB and NOB were Nitrosococcus and Nitrospira, which accounted for 90% and 91%, respectively, under point aeration, and the diversity of nitrifying bacteria was lower than under step aeration. Point aeration was selective of nitrifying bacteria. The abundance of NOB was greater than that of AOB in both of the operation modes, and complete transformation of NH4(+) N to NO3(-)-N was observed without NO2(-)-N accumulation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Arsenite and ferrous iron oxidation linked to chemolithotrophic denitrification for the immobilization of arsenic in anoxic environments

USGS Publications Warehouse

Sun, W.; Sierra-Alvarez, R.; Milner, L.; Oremland, R.; Field, J.A.

2009-01-01

The objective of this study was to explore a bioremediation strategy based on injecting NO3- to support the anoxic oxidation of ferrous iron (Fe(II)) and arsenite (As(III)) in the subsurface as a means to immobilize As in the form of arsenate (As(V)) adsorbed onto biogenic ferric (Fe(III)) (hydr)oxides. Continuous flows and filled columns were used to simulate a natural anaerobic groundwater and sediment system with co-occurring As(III) and Fe(II) in the presence (column SF1) or absence (column SF2) of nitrate, respectively. During operation for 250 days, the average influent arsenic concentration of 567 ??g L-1 was reduced to 10.6 (??9.6) ??g L-1 in the effluent of column SF1. The cumulative removal of Fe(II) and As(III) in SF1 was 6.5 to 10-fold higher than that in SF2. Extraction and measurement of the mass of iron and arsenic immobilized on the sand packing of the columns were close to the iron and arsenic removed from the aqueous phase during column operation. The dominant speciation of the immobilized iron and arsenic was Fe(III) and As(V) in SF1, compared with Fe(II) and As(III) in SF2. The speciation was confirmed by X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS). The results indicate that microbial oxidation of As(III) and Fe(II) linked to denitrification resulted in the enhanced immobilization of aqueous arsenic in anaerobic environments by forming Fe(III) (hydr)oxide coated sands with adsorbed As(V). ?? 2009 American Chemical Society.

Back To Bacteria.

ERIC Educational Resources Information Center

Flannery, Maura C.

1997-01-01

Explores new research about bacteria. Discusses bacterial genomes, archaea, unusual environments, evolution, pathogens, bacterial movement, biofilms, bacteria in the body, and a bacterial obsession. Contains 29 references. (JRH)

Incorporation of Metals into Calcite in a Deep Anoxic Granite Aquifer.

PubMed

Drake, Henrik; Mathurin, Frédéric A; Zack, Thomas; Schäfer, Thorsten; Roberts, Nick Mw; Whitehouse, Martin; Karlsson, Andreas; Broman, Curt; Åström, Mats E

2018-01-16

Understanding metal scavenging by calcite in deep aquifers in granite is of importance for deciphering and modeling hydrochemical fluctuations and water-rock interaction in the upper crust and for retention mechanisms associated with underground repositories for toxic wastes. Metal scavenging into calcite has generally been established in the laboratory or in natural environments that cannot be unreservedly applied to conditions in deep crystalline rocks, an environment of broad interest for nuclear waste repositories. Here, we report a microanalytical study of calcite precipitated over a period of 17 years from anoxic, low-temperature (14 °C), neutral (pH: 7.4-7.7), and brackish (Cl: 1700-7100 mg/L) groundwater flowing in fractures at >400 m depth in granite rock. This enabled assessment of the trace metal uptake by calcite under these deep-seated conditions. Aquatic speciation modeling was carried out to assess influence of metal complexation on the partitioning into calcite. The resulting environment-specific partition coefficients were for several divalent ions in line with values obtained in controlled laboratory experiments, whereas for several other ions they differed substantially. High absolute uptake of rare earth elements and U(IV) suggests that coprecipitation into calcite can be an important sink for these metals and analogousactinides in the vicinity of geological repositories.

SAR11 bacteria linked to ocean anoxia and nitrogen loss

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsementzi, Despina; Wu, Jieying; Deutsch, Samuel

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N 2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here in this paper, genomic analysis of single cells from the world's largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductasesmore » (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. Finally, these results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth's most abundant organismal group.« less

SAR11 bacteria linked to ocean anoxia and nitrogen loss

DOE PAGES

Tsementzi, Despina; Wu, Jieying; Deutsch, Samuel; ...

2016-08-03

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N 2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here in this paper, genomic analysis of single cells from the world's largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductasesmore » (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. Finally, these results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth's most abundant organismal group.« less

Large CH4 production fueled by autochthonous OC in an anoxic sediment

NASA Astrophysics Data System (ADS)

Grasset, Charlotte; Mendonça, Raquel; Villamor Saucedo, Gabriella; Sobek, Sebastian

2017-04-01

River damming and human-induced eutrophication both affect river and lake functioning, increase organic carbon (OC) sedimentation rates and generate anoxic conditions in bottom waters. Under these conditions, OC in sediments is decomposed into CO2 and CH4, a high potential greenhouse gas. It has been shown that the decomposition of land-derived (allochthonous) OC is inhibited at anoxic conditions, compared to OC internally produced (autochthonous). However, the overall extent and end products (CO2 or CH4) of anoxic decomposition remain poorly known for different types of OC, making it difficult to judge the effect of river damming and eutrophication on greenhouse gas emissions from inland waters. We incubated different types of allochthonous OC (terrestrial plants) and autochthonous OC (phytoplankton and aquatic vascular plants) in an anoxic sediment during 130 days. We aimed to test 1) if this addition of relatively fresh OC resulted in an increase of CH4 production and 2) if autochthonous OC would produce more CH4 than allochthonous OC. We assessed the contribution to CH4 production of the different OC sources (i.e. sediment or added OC) with stable isotope measurements. We found that the addition of relatively fresh OC greatly increased CH4 production. Autochthonous OC generally produced more CH4 than allochthonous OC, but the overall extent of CH4 production was highly variable between the different autochthonous OC types. The d13C-CH4 measurements indicated that CH4 originated exclusively from the added OC. We conclude that the production of CH4 is likely to to be high in eutrophic as well as in artificial lakes, especially when these systems have anoxic bottom waters and high internal primary productivity and thus a high supply of autochthonous OC to the sediment. The current expansion of reservoir construction in concert with almost globally prevalent anthropogenic eutrophication are therefore likely to increase CH4 production in inland waters.

Methanotrophic bacteria.

PubMed Central

Hanson, R S; Hanson, T E

1996-01-01

Methane-utilizing bacteria (methanotrophs) are a diverse group of gram-negative bacteria that are related to other members of the Proteobacteria. These bacteria are classified into three groups based on the pathways used for assimilation of formaldehyde, the major source of cell carbon, and other physiological and morphological features. The type I and type X methanotrophs are found within the gamma subdivision of the Proteobacteria and employ the ribulose monophosphate pathway for formaldehyde assimilation, whereas type II methanotrophs, which employ the serine pathway for formaldehyde assimilation, form a coherent cluster within the beta subdivision of the Proteobacteria. Methanotrophic bacteria are ubiquitous. The growth of type II bacteria appears to be favored in environments that contain relatively high levels of methane, low levels of dissolved oxygen, and limiting concentrations of combined nitrogen and/or copper. Type I methanotrophs appear to be dominant in environments in which methane is limiting and combined nitrogen and copper levels are relatively high. These bacteria serve as biofilters for the oxidation of methane produced in anaerobic environments, and when oxygen is present in soils, atmospheric methane is oxidized. Their activities in nature are greatly influenced by agricultural practices and other human activities. Recent evidence indicates that naturally occurring, uncultured methanotrophs represent new genera. Methanotrophs that are capable of oxidizing methane at atmospheric levels exhibit methane oxidation kinetics different from those of methanotrophs available in pure cultures. A limited number of methanotrophs have the genetic capacity to synthesize a soluble methane monooxygenase which catalyzes the rapid oxidation of environmental pollutants including trichloroethylene. PMID:8801441

Nitrogen removal and microbial communities in a three-stage system simulating a riparian environment.

PubMed

Wang, Ziyuan; Wang, Zhixin; Pei, Yuansheng

2014-06-01

The riparian zone is an active interface for nitrogen removal, in which nitrogen transformations by microorganisms have not been valued. In this study, a three-stage system was constructed to simulate the riparian zone environments, and nitrogen removal as well as the microbial community was investigated in this 'engineered riparian system'. The results demonstrated that stage 1 of this system accounted for 41-51 % of total nitrogen removal. Initial ammonium loading and redox potential significantly impacted the nitrogen removal performances. Stages 1 and 2 were both composed of an anoxic/oxic (A/O) zone and an anaerobic column. The A/O zone removed most of the ammonium load (6.8 g/m(2)/day), while the anaerobic column showed a significant nitrate removal rate (11.1 g/m(2)/day). Molecular biological analysis demonstrated that bacterial diversity was high in the A/O zones, where ammonium-oxidizing bacteria and nitrite-oxidizing bacteria accounted for 8.42 and 3.32 % of the bacterial population, respectively. The denitrifying bacteria Acidovorax sp. and the nitrifying bacteria Nitrosospira/Nitrosomonas were the predominant microorganisms in this engineered riparian system. This three-stage system was established to achieve favorable nitrogen removal and the microbial community in the system was also retained. This investigation should deepen our understanding of biological nitrogen removal in engineered riparian zones.

Microbial ecology of deep-sea hypersaline anoxic basins.

PubMed

Merlino, Giuseppe; Barozzi, Alan; Michoud, Grégoire; Ngugi, David Kamanda; Daffonchio, Daniele

2018-07-01

Deep hypersaline anoxic basins (DHABs) are unique water bodies occurring within fractures at the bottom of the sea, where the dissolution of anciently buried evaporites created dense anoxic brines that are separated by a chemocline/pycnocline from the overlying oxygenated deep-seawater column. DHABs have been described in the Gulf of Mexico, the Mediterranean Sea, the Black Sea and the Red Sea. They are characterized by prolonged historical separation of the brines from the upper water column due to lack of mixing and by extreme conditions of salinity, anoxia, and relatively high hydrostatic pressure and temperatures. Due to these combined selection factors, unique microbial assemblages thrive in these polyextreme ecosystems. The topological localization of the different taxa in the brine-seawater transition zone coupled with the metabolic interactions and niche adaptations determine the metabolic functioning and biogeochemistry of DHABs. In particular, inherent metabolic strategies accompanied by genetic adaptations have provided insights on how prokaryotic communities can adapt to salt-saturated conditions. Here, we review the current knowledge of the diversity, genomics, metabolisms and ecology of prokaryotes in DHABs.

Sulfate reducing bacteria in microbial mats: Changing paradigms, new discoveries

NASA Astrophysics Data System (ADS)

Baumgartner, L. K.; Reid, R. P.; Dupraz, C.; Decho, A. W.; Buckley, D. H.; Spear, J. R.; Przekop, K. M.; Visscher, P. T.

2006-03-01

Sulfate reducing bacteria (SRB) have existed throughout much of Earth's history and remain major contributors to carbon cycling in modern systems. Despite their importance, misconceptions about SRB are prevalent. In particular, SRB are commonly thought to lack oxygen tolerance and to exist only in anoxic environments. Through the last two decades, researchers have discovered that SRB can, in fact, tolerate and even respire oxygen. Investigations of microbial mat systems have demonstrated that SRB are both abundant and active in the oxic zones of mats. Additionally, SRB have been found to be highly active in the lithified zones of microbial mats, suggesting a connection between sulfate reduction and mat lithification. In the present paper, we review recent research on SRB distribution and present new preliminary findings on both the diversity and distribution of δ-proteobacterial SRB in lithifying and non-lithifying microbial mat systems. These preliminary findings indicate the unexplored diversity of SRB in a microbial mat system and demonstrate the close microspatial association of SRB and cyanobacteria in the oxic zone of the mat. Possible mechanisms and further studies to elucidate mechanisms for carbonate precipitation via sulfate reduction are also discussed.

Theoretical analysis of the cost of antagonistic activity for aquatic bacteria in oligotrophic environments.

PubMed

Aguirre-von-Wobeser, Eneas; Eguiarte, Luis E; Souza, Valeria; Soberón-Chávez, Gloria

2015-01-01

Many strains of bacteria produce antagonistic substances that restrain the growth of others, and potentially give them a competitive advantage. These substances are commonly released to the surrounding environment, involving metabolic costs in terms of energy and nutrients. The rate at which these molecules need to be produced to maintain a certain amount of them close to the producing cell before they are diluted into the environment has not been explored so far. To understand the potential cost of production of antagonistic substances in water environments, we used two different theoretical approaches. Using a probabilistic model, we determined the rate at which a cell needs to produce individual molecules in order to keep on average a single molecule in its vicinity at all times. For this minimum protection, a cell would need to invest 3.92 × 10(-22) kg s(-1) of organic matter, which is 9 orders of magnitude lower than the estimated expense for growth. Next, we used a continuous model, based on Fick's laws, to explore the production rate needed to sustain minimum inhibitory concentrations around a cell, which would provide much more protection from competitors. In this scenario, cells would need to invest 1.20 × 10(-11) kg s(-1), which is 2 orders of magnitude higher than the estimated expense for growth, and thus not sustainable. We hypothesize that the production of antimicrobial compounds by bacteria in aquatic environments lies between these two extremes.

Anoxic conditions drive phosphorus limitation in humid tropical forest soil microorganisms

NASA Astrophysics Data System (ADS)

Gross, A.; Pett-Ridge, J.; Weber, P. K.; Blazewicz, S.; Silver, W. L.

2017-12-01

The elemental stoichiometry of carbon (C), nitrogen (N) and phosphorus (P) of soil microorganisms (C:N:P ratios) regulates transfers of energy and nutrients to higher trophic levels. In humid tropical forests that grow on P-depleted soils, the ability of microbes to concentrate P from their surroundings likely plays a critical role in P-retention and ultimately in forest productivity. Models predict that climate change will cause dramatic changes in rainfall patterns in the humid tropics and field studies have shown these changes can affect the redox state of tropical forest soils, influencing soil respiration and biogeochemical cycling. However, the responses of soil microorganisms to changing environmental conditions are not well known. Here, we incubated humid tropical soils under oxic or anoxic conditions with substrates differing in both C:P stoichiometry and lability, to assess how soil microorganisms respond to different redox regimes. We found that under oxic conditions, microbial C:P ratios were similar to the global optimal ratio (55:1), indicating most microbial cells can adapt to persistent aerated conditions in these soils. However, under anoxic conditions, the ability of soil microbes to acquire soil P declined and their C:P ratios shifted away from the optimal ratio. NanoSIMS elemental imaging of single cells extracted from soil revealed that under anoxic conditions, C:P ratios were above the microbial optimal value in 83% of the cells, in comparison to 41% under oxic conditions. These data suggest microbial growth efficiency switched from being energy limited under oxic conditions to P-limited under anoxic conditions, indicating that, microbial growth in low P humid tropical forests soils may be most constrained by P-limitation when conditions are oxygen-limited. We suggest that differential microbial responses to soil redox states could have important implications for productivity of humid tropical forests under future climate scenarios.

Potential impacts of silver nanoparticles on bacteria in the aquatic environment.

PubMed

Sheng, Zhiya; Liu, Yang

2017-04-15

It is inevitable that nano-silver will be released into the environment. Therefore, there is an urgent need to better understand the effects of silver nanoparticles (Ag-NPs) on microbes in natural and engineered environments. The most remarkable gap in our knowledge on this lies on the low Ag-NPs dose side. This review summarized studies on the effects of Ag-NPs on bacteria from simple to complicated aquatic systems. A hormetic model with a narrow stimulatory zone has been proposed based on both experimental phenomenon and the potential mechanisms of the observed effects. Spectrum of the stimulating zone depends on Ag-NP properties, bacterial types and environmental conditions tested. This may become a concern in terms of Ag-NP disposal, and further research is required to build a sophisticated toxicity model for Ag-NPs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Using Biogenic Sulfur Gases as Remotely Detectable Biosignatures on Anoxic Planets

PubMed Central

Meadows, Victoria S.; Claire, Mark W.; Kasting, James F.

2011-01-01

Abstract We used one-dimensional photochemical and radiative transfer models to study the potential of organic sulfur compounds (CS2, OCS, CH3SH, CH3SCH3, and CH3S2CH3) to act as remotely detectable biosignatures in anoxic exoplanetary atmospheres. Concentrations of organic sulfur gases were predicted for various biogenic sulfur fluxes into anoxic atmospheres and were found to increase with decreasing UV fluxes. Dimethyl sulfide (CH3SCH3, or DMS) and dimethyl disulfide (CH3S2CH3, or DMDS) concentrations could increase to remotely detectable levels, but only in cases of extremely low UV fluxes, which may occur in the habitable zone of an inactive M dwarf. The most detectable feature of organic sulfur gases is an indirect one that results from an increase in ethane (C2H6) over that which would be predicted based on the planet's methane (CH4) concentration. Thus, a characterization mission could detect these organic sulfur gases—and therefore the life that produces them—if it could sufficiently quantify the ethane and methane in the exoplanet's atmosphere. Key Words: Exoplanets—Biosignatures—Anoxic atmospheres—Planetary atmospheres—Remote life detection—Photochemistry. Astrobiology 11, 419–441. PMID:21663401

Novel Pelagic Iron-Oxidizing Zetaproteobacteria from the Chesapeake Bay Oxic-Anoxic Transition Zone.

PubMed

Chiu, Beverly K; Kato, Shingo; McAllister, Sean M; Field, Erin K; Chan, Clara S

2017-01-01

Chemolithotrophic iron-oxidizing bacteria (FeOB) could theoretically inhabit any environment where Fe(II) and O 2 (or nitrate) coexist. Until recently, marine Fe-oxidizing Zetaproteobacteria had primarily been observed in benthic and subsurface settings, but not redox-stratified water columns. This may be due to the challenges that a pelagic lifestyle would pose for Zetaproteobacteria, given low Fe(II) concentrations in modern marine waters and the possibility that Fe oxyhydroxide biominerals could cause cells to sink. However, we recently cultivated Zetaproteobacteria from the Chesapeake Bay oxic-anoxic transition zone, suggesting that they can survive and contribute to biogeochemical cycling in a stratified estuary. Here we describe the isolation, characterization, and genomes of two new species, Mariprofundus aestuarium CP-5 and Mariprofundus ferrinatatus CP-8, which are the first Zetaproteobacteria isolates from a pelagic environment. We looked for adaptations enabling strains CP-5 and CP-8 to overcome the challenges of living in a low Fe redoxcline with frequent O 2 fluctuations due to tidal mixing. We found that the CP strains produce distinctive dreadlock-like Fe oxyhydroxide structures that are easily shed, which would help cells maintain suspension in the water column. These oxides are by-products of Fe(II) oxidation, likely catalyzed by the putative Fe(II) oxidase encoded by the cyc2 gene, present in both CP-5 and CP-8 genomes; the consistent presence of cyc2 in all microaerophilic FeOB and other FeOB genomes supports its putative role in Fe(II) oxidation. The CP strains also have two gene clusters associated with biofilm formation (Wsp system and the Widespread Colonization Island) that are absent or rare in other Zetaproteobacteria. We propose that biofilm formation enables the CP strains to attach to FeS particles and form flocs, an advantageous strategy for scavenging Fe(II) and developing low [O 2 ] microenvironments within more oxygenated waters

Novel Pelagic Iron-Oxidizing Zetaproteobacteria from the Chesapeake Bay Oxic–Anoxic Transition Zone

PubMed Central

Chiu, Beverly K.; Kato, Shingo; McAllister, Sean M.; Field, Erin K.; Chan, Clara S.

2017-01-01

Chemolithotrophic iron-oxidizing bacteria (FeOB) could theoretically inhabit any environment where Fe(II) and O2 (or nitrate) coexist. Until recently, marine Fe-oxidizing Zetaproteobacteria had primarily been observed in benthic and subsurface settings, but not redox-stratified water columns. This may be due to the challenges that a pelagic lifestyle would pose for Zetaproteobacteria, given low Fe(II) concentrations in modern marine waters and the possibility that Fe oxyhydroxide biominerals could cause cells to sink. However, we recently cultivated Zetaproteobacteria from the Chesapeake Bay oxic–anoxic transition zone, suggesting that they can survive and contribute to biogeochemical cycling in a stratified estuary. Here we describe the isolation, characterization, and genomes of two new species, Mariprofundus aestuarium CP-5 and Mariprofundus ferrinatatus CP-8, which are the first Zetaproteobacteria isolates from a pelagic environment. We looked for adaptations enabling strains CP-5 and CP-8 to overcome the challenges of living in a low Fe redoxcline with frequent O2 fluctuations due to tidal mixing. We found that the CP strains produce distinctive dreadlock-like Fe oxyhydroxide structures that are easily shed, which would help cells maintain suspension in the water column. These oxides are by-products of Fe(II) oxidation, likely catalyzed by the putative Fe(II) oxidase encoded by the cyc2 gene, present in both CP-5 and CP-8 genomes; the consistent presence of cyc2 in all microaerophilic FeOB and other FeOB genomes supports its putative role in Fe(II) oxidation. The CP strains also have two gene clusters associated with biofilm formation (Wsp system and the Widespread Colonization Island) that are absent or rare in other Zetaproteobacteria. We propose that biofilm formation enables the CP strains to attach to FeS particles and form flocs, an advantageous strategy for scavenging Fe(II) and developing low [O2] microenvironments within more oxygenated waters

[Analysis of carbon balance and study on mechanism in anoxic-oxic-settling-anaerobic sludge reduction process].

PubMed

Zhai, Xiao-Min; Gao, Xu; Zhang, Man-Man; Jia, Li; Guo, Jin-Song

2012-07-01

In order to deeply explore the mechanism of sludge reduction in OSA system, carbon balance was performed in an anoxic-oxic-settling-anaerobic (A + OSA) system and a reference AO system to investigate effects of inserting a sludge holding tank in sludge cycle line on the sludge reduction process. Meanwhile, carbon mass change in each reaction unit was identified in terms of solid, liquid and gas phases. The causes of excess sludge reduction in A + OSA system were deduced. The carbon balance results show that when the hydraulic retention time in the sludge holding tank is 7.14 h, carbon percent in solid phase of the sludge reduction system is nearly 50% higher than that of the reference system, supporting the consequence that sludge reduction rate of 49.98% had been achieved. The insertion of a sludge holding tank in the sludge return circuit can be effective in sludge reduction. Carbon changes in each unit reveal that the amount of carbon consumed for biosynthesis in the anoxic and oxic tanks (main reaction zone) of the sludge reduction system is higher than in that of the reference system. Sludge decay is observed in the sludge holding tank. Furthermore, CH4 released from the sludge holding tank is significantly higher than that from the main reaction zone. The DGGE profiles show that there are hydrolytic-fermentative bacteria in the sludge holding tank related to sludge decay. The excess sludge reduction in the A + OSA system could be a result of the combination of sludge decay in the sludge holding tank and sludge compensatory growth in the main reaction cell.

Horizontal gene transfer between bacteria.

PubMed

Heuer, Holger; Smalla, Kornelia

2007-01-01

Horizontal gene transfer (HGT) refers to the acquisition of foreign genes by organisms. The occurrence of HGT among bacteria in the environment is assumed to have implications in the risk assessment of genetically modified bacteria which are released into the environment. First, introduced genetic sequences from a genetically modified bacterium could be transferred to indigenous micro-organisms and alter their genome and subsequently their ecological niche. Second, the genetically modified bacterium released into the environment might capture mobile genetic elements (MGE) from indigenous micro-organisms which could extend its ecological potential. Thus, for a risk assessment it is important to understand the extent of HGT and genome plasticity of bacteria in the environment. This review summarizes the present state of knowledge on HGT between bacteria as a crucial mechanism contributing to bacterial adaptability and diversity. In view of the use of GM crops and microbes in agricultural settings, in this mini-review we focus particularly on the presence and role of MGE in soil and plant-associated bacteria and the factors affecting gene transfer.

Growth of magnetotactic sulfate-reducing bacteria in oxygen concentration gradient medium.

PubMed

Lefèvre, Christopher T; Howse, Paul A; Schmidt, Marian L; Sabaty, Monique; Menguy, Nicolas; Luther, George W; Bazylinski, Dennis A

2016-12-01

Although dissimilatory sulfate-reducing bacteria (SRB) are generally described as strictly anaerobic organisms with regard to growth, several reports have shown that some SRB, particularly Desulfovibrio species, are quite resistant to O 2 . For example, SRB remain viable in many aerobic environments while some even reduce O 2 to H 2 O. However, reproducible aerobic growth of SRB has not been unequivocally documented. Desulfovibrio magneticus is a SRB that is also a magnetotactic bacterium (MTB). MTB biomineralize magnetosomes which are intracellular, membrane-bounded, magnetic iron mineral crystals. The ability of D. magneticus to grow aerobically in several different media under air where an O 2 concentration gradient formed, or under O 2 -free N 2 gas was tested. Under air, cells grew as a microaerophilic band of cells at the oxic-anoxic interface in media lacking sulfate. These results show that D. magneticus is capable of aerobic growth with O 2 as a terminal electron acceptor. This is the first report of consistent, reproducible aerobic growth of SRB. This finding is critical in determining important ecological roles SRB play in the environment. Interestingly, the crystal structure of the magnetite crystals of D. magneticus grown under microaerobic conditions showed significant differences compared with those produced anaerobically providing more evidence that environmental parameters influence magnetosome formation. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Effect of Free Ammonia, Free Nitrous Acid, and Alkalinity on the Partial Nitrification of Pretreated Pig Slurry, Using an Alternating Oxic/Anoxic SBR

PubMed Central

Hsieh, Chia-Fang; Guerrero, Lorna; Méndez, Ramón; Mosquera-Corral, Anuska; Vidal, Gladys

2017-01-01

The effect of free ammonia (NH3 or FA), free nitrous acid (HNO2 or FNA), and total alkalinity (TA) on the performance of a partial nitrification (PN) sequencing batch reactor (SBR) treating anaerobically pretreated pig slurry was studied. The SBR was operated under alternating oxic/anoxic (O/A) conditions and was fed during anoxic phases. This strategy allowed using organic matter to partially remove nitrite (NO2−) and nitrate (NO3−) generated during oxic phases. The desired NH4+ to NO2− ratio of 1.3 g N/g N was obtained when an Ammonium Loading Rate (ALR) of 0.09 g NH4+-N/L·d was applied. The system was operated at a solid retention time (SRT) of 15–20 d and dissolved oxygen (DO) levels higher than 3 mg O2/L during the whole operational period. PN mainly occurred caused by the inhibitory effect of FNA on nitrite oxidizing bacteria (NOB). Once HNO2 concentration was negligible, NH4+ was fully oxidized to NO3− in spite of the presence of FA. The use of biomass acclimated to ammonium as inoculum avoided a possible effect of FA on NOB activity. PMID:29018815

Millimeter waves or extremely high frequency electromagnetic fields in the environment: what are their effects on bacteria?

PubMed

Soghomonyan, Diana; Trchounian, Karen; Trchounian, Armen

2016-06-01

Millimeter waves (MMW) or electromagnetic fields of extremely high frequencies at low intensity is a new environmental factor, the level of which is increased as technology advance. It is of interest that bacteria and other cells might communicate with each other by electromagnetic field of sub-extremely high frequency range. These MMW affected Escherichia coli and many other bacteria, mainly depressing their growth and changing properties and activity. These effects were non-thermal and depended on different factors. The significant cellular targets for MMW effects could be water, cell plasma membrane, and genome. The model for the MMW interaction with bacteria is suggested; a role of the membrane-associated proton FOF1-ATPase, key enzyme of bioenergetic relevance, is proposed. The consequences of MMW interaction with bacteria are the changes in their sensitivity to different biologically active chemicals, including antibiotics. Novel data on MMW effects on bacteria and their sensitivity to different antibiotics are presented and discussed; the combined action of MMW and antibiotics resulted with more strong effects. These effects are of significance for understanding changed metabolic pathways and distinguish role of bacteria in environment; they might be leading to antibiotic resistance in bacteria. The effects might have applications in the development of technique, therapeutic practices, and food protection technology.

Microbial diversity of an anoxic zone of a hydroelectric power station reservoir in Brazilian Amazonia.

PubMed

Graças, Diego A; Miranda, Paulo R; Baraúna, Rafael A; McCulloch, John A; Ghilardi, Rubens; Schneider, Maria Paula C; Silva, Artur

2011-11-01

Microbial diversity was evaluated in an anoxic zone of Tucuruí Hydroelectric Power Station reservoir in Brazilian Amazonia using a culture-independent approach by amplifying and sequencing fragments of the 16S rRNA gene using metagenomic DNA as a template. Samples obtained from the photic, aphotic (40 m) and sediment (60 m) layers were used to construct six 16S rDNA libraries containing a total of 1,152 clones. The sediment, aphotic and photic layers presented 64, 33 and 35 unique archaeal operational taxonomic units (OTUs). The estimated richness of these layers was evaluated to be 153, 106 and 79 archaeal OTUs, respectively, using the abundance-based coverage estimator (ACE) and 114, 83 and 77 OTUs using the Chao1 estimator. For bacterial sequences, 114, 69 and 57 OTUs were found in the sediment, aphotic and photic layers, which presented estimated richnesses of 1,414, 522 and 197 OTUs (ACE) and 1,059, 1,014 and 148 OTUs (Chao1), respectively. Phylogenetic analyses of the sequences obtained revealed a high richness of microorganisms which participate in the carbon cycle, namely, methanogenic archaea and methanotrophic proteobacteria. Most sequences obtained belong to non-culturable prokaryotes. The present study offers the first glimpse of the huge microbial diversity of an anoxic area of a man-made lacustrine environment in the tropics.

Distribution, genetic diversity and antibiotic resistance of clinically important bacteria from the environment of a tertiary hospital.

PubMed

Phoon, Hannah Y P; Hussin, Hazilawati; Hussain, Baizurah Mohd; Lim, Shu Yong; Woon, Jia Jie; Er, Yi Xian; Thong, Kwai Lin

2018-03-11

Hospital environments are potential reservoirs of bacteria associated with nosocomial infections. Here, we determined the distribution of cultivable environmental bacteria of clinical importance from a Malaysian tertiary hospital and to investigate their resistotypes and genotypes. Swab and fluid samples (n=358) from healthcare workers' hands, frequently touched surfaces, medical equipment, patients' immediate surroundings, ward sinks and toilets and solutions or fluids of 12 selected wards were collected. Biochemical tests, PCR and 16S rRNA sequencing were used for identification after isolation from CHROMagar TM Orientation medium. Clinically important bacteria such as Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter spp., Pseudomonas aeruginosa, and Enterobacter spp. were further characterised by disk diffusion method and REP-PCR. The 32 Gram negative and 21 Gram positive bacteria species identified were widely distributed in the hospital environment. Staphylococci were predominant followed by Bacillus spp., and P. aeruginosa. Frequently touched surfaces, medical equipment and ward sinks and toilets were the top three sources of bacterial species. Nine S. aureus, four Acinetobacter spp., one K. pneumoniae, and one Enterobacter spp., were multidrug resistant (MDR). The ESKAPE organisms were genetically diverse and widely dispersed across the hospital wards. An MDR MRSA clone was detected in a surgical ward isolation room. The large variety of cultivable, clinically important bacteria, especially the genetically related MDR S. aureus, K. pneumoniae, Acinetobacter spp., and Enterobacter spp. from various sampling sites indicated that the surfaces and fomites in the hospital were potential exogenous sources of nosocomial infections in the hospital. Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

Microbial fouling and corrosion of carbon steel in deep anoxic alkaline groundwater.

PubMed

Rajala, Pauliina; Bomberg, Malin; Vepsäläinen, Mikko; Carpén, Leena

2017-02-01

Understanding the corrosion of carbon steel materials of low and intermediate level radioactive waste under repository conditions is crucial to ensure the safe storage of radioactive contaminated materials. The waste will be in contact with the concrete of repository silos and storage containers, and eventually with groundwater. In this study, the corrosion of carbon steel under repository conditions as well as the microbial community forming biofilm on the carbon steel samples, consisting of bacteria, archaea, and fungi, was studied over a period of three years in a groundwater environment with and without inserted concrete. The number of biofilm forming bacteria and archaea was 1,000-fold lower, with corrosion rates 620-times lower in the presence of concrete compared to the natural groundwater environment. However, localized corrosion was detected in the concrete-groundwater environment indicating the presence of local microenvironments where the conditions for pitting corrosion were favorable.

Alternating anoxic feast/aerobic famine condition for improving granular sludge formation in sequencing batch airlift reactor at reduced aeration rate.

PubMed

Wan, Junfeng; Bessière, Yolaine; Spérandio, Mathieu

2009-12-01

In this study the influence of a pre-anoxic feast period on granular sludge formation in a sequencing batch airlift reactor is evaluated. Whereas a purely aerobic SBR was operated as a reference (reactor R2), another reactor (R1) was run with a reduced aeration rate and an alternating anoxic-aerobic cycle reinforced by nitrate feeding. The presence of pre-anoxic phase clearly improved the densification of aggregates and allowed granular sludge formation at reduced air flow rate (superficial air velocity (SAV)=0.63cms(-1)). A low sludge volume index (SVI(30)=45mLg(-1)) and a high MLSS concentration (9-10gL(-1)) were obtained in the anoxic/aerobic system compared to more conventional results for the aerobic reactor. A granular sludge was observed in the anoxic/aerobic system whilst only flocs were observed in the aerobic reference even when operated at a high aeration rate (SAV=2.83cms(-1)). Nitrification was maintained efficiently in the anoxic/aerobic system even when organic loading rate (OLR) was increased up to 2.8kgCODm(-3)d(-1). In the contrary nitrification was unstable in the aerobic system and dropped at high OLR due to competition between autotrophic and heterotrophic growth. The presence of a pre-anoxic period positively affected granulation process via different mechanisms: enhancing heterotrophic growth/storage deeper in the internal anoxic layer of granule, reducing the competition between autotrophic and heterotrophic growth. These processes help to develop dense granular sludge at a moderate aeration rate. This tends to confirm that oxygen transfer is the most limiting factor for granulation at reduced aeration. Hence the use of an alternative electron acceptor (nitrate or nitrite) should be encouraged during feast period for reducing energy demand of the granular sludge process.

Effects of Methyl Jasmonate on Acute Stress Responses in Mice Subjected to Forced Swim and Anoxic Tests

PubMed Central

Aluko, Oritoke M.; Umukoro, Solomon; Annafi, Olajide S.; Adewole, Folashade A.; Omorogbe, Osarume

2015-01-01

Methyl jasmonate (MJ) is an anti-stress hormone released by plants in response to external stressors and aids adaptation to stress. In this study, we evaluated the anti-stress activity of MJ using the forced swim endurance test (FSET) and anoxic tolerance test in mice. Male Swiss mice were given MJ (25–100 mg/kg, i.p) 30 min before the FSET and anoxic test were carried out. The first occurrence of immobility, duration of immobility, time spent in active swimming, and latency to exhaustion were assessed in the FSET. The onset to anoxic convulsion was measured in the anoxic tolerance test. MJ significantly (p < 0.05) delayed the first occurrence of immobility and shortened the period of immobility, which indicates anti-stress property. MJ also increased the time spent in active swimming and prolonged the latency to exhaustion, which further suggests anti-stress activity. In addition, it also exhibited anti-stress property as evidenced by prolonged latency to first appearance of anoxic convulsions. The results of this study suggest that MJ demonstrated anti-stress activity and may be useful as an energizer in times of body weakness or exhaustion. Although more studies are necessary before concluding on how MJ exerts its anti-stress activity, the present data suggest an action similar to adaptogens in boosting energy and resilience in the face of stress. PMID:26839844

The ecology and biotechnology of sulphate-reducing bacteria.

PubMed

Muyzer, Gerard; Stams, Alfons J M

2008-06-01

Sulphate-reducing bacteria (SRB) are anaerobic microorganisms that use sulphate as a terminal electron acceptor in, for example, the degradation of organic compounds. They are ubiquitous in anoxic habitats, where they have an important role in both the sulphur and carbon cycles. SRB can cause a serious problem for industries, such as the offshore oil industry, because of the production of sulphide, which is highly reactive, corrosive and toxic. However, these organisms can also be beneficial by removing sulphate and heavy metals from waste streams. Although SRB have been studied for more than a century, it is only with the recent emergence of new molecular biological and genomic techniques that we have begun to obtain detailed information on their way of life.

Recovery of Humic-Reducing Bacteria from a Diversity of Environments

PubMed Central

Coates, John D.; Ellis, Debra J.; Blunt-Harris, Elizabeth L.; Gaw, Catherine V.; Roden, Eric E.; Lovley, Derek R.

1998-01-01

To evaluate which microorganisms might be responsible for microbial reduction of humic substances in sedimentary environments, humic-reducing bacteria were isolated from a variety of sediment types. These included lake sediments, pristine and contaminated wetland sediments, and marine sediments. In each of the sediment types, all of the humic reducers recovered with acetate as the electron donor and the humic substance analog, 2,6-anthraquinone disulfonate (AQDS), as the electron acceptor were members of the family Geobacteraceae. This was true whether the AQDS-reducing bacteria were enriched prior to isolation on solid media or were recovered from the highest positive dilutions of sediments in liquid media. All of the isolates tested not only conserved energy to support growth from acetate oxidation coupled to AQDS reduction but also could oxidize acetate with highly purified soil humic acids as the sole electron acceptor. All of the isolates tested were also able to grow with Fe(III) serving as the sole electron acceptor. This is consistent with previous studies that have suggested that the capacity for Fe(III) reduction is a common feature of all members of the Geobacteraceae. These studies demonstrate that the potential for microbial humic substance reduction can be found in a wide variety of sediment types and suggest that Geobacteraceae species might be important humic-reducing organisms in sediments. PMID:9546186

Magnetotactic bacteria and magnetosomes - Scope and challenges.

PubMed

Jacob, Jobin John; Suthindhiran, K

2016-11-01

Geomagnetism aided navigation has been demonstrated by certain organisms which allows them to identify a particular location using magnetic field. This attractive technique to recognize the course was earlier exhibited in numerous animals, for example, birds, insects, reptiles, fishes and mammals. Magnetotactic bacteria (MTB) are one of the best examples for magnetoreception among microorganisms as the magnetic mineral functions as an internal magnet and aid the microbe to move towards the water columns in an oxic-anoxic interface (OAI). The ability of MTB to biomineralize the magnetic particles (magnetosomes) into uniform nano-sized, highly crystalline structure with uniform magnetic properties has made the bacteria an important topic of research. The superior properties of magnetosomes over chemically synthesized magnetic nanoparticles made it an attractive candidate for potential applications in microbiology, biophysics, biochemistry, nanotechnology and biomedicine. In this review article, the scope of MTB, magnetosomes and its challenges in research and industrial application have been discussed in brief. This article mainly focuses on the application based on the magnetotactic behaviour of MTB and magnetosomes in different areas of modern science. Copyright © 2016 Elsevier B.V. All rights reserved.

Effect of temperature on anoxic sulfide oxidation and denitrification in the bulk wastewater phase of sewer networks.

PubMed

Mathioudakis, V L; Aivasidis, A

2009-01-01

Artificial dosage of nitrate in sewer networks is considered as one of the most effective methods for odor and corrosion control. However, there is limited knowledge on the effect of temperature on the transformations that takes place during anoxic conditions. Thus, two groups of batch experiments were conducted to gain insight in the involved processes in bulk phase of a septic municipal wastewater. It can be concluded that sewer denitrification, in bulk phase, can be simplified in three stages. According to the experimental results, nitrate or nitrite is utilized for autotrophic denitrification with sulfide, while heterotrophic utilization is initiated after the completion of anoxic sulfide oxidation. Moreover, temperature is proved to have a significant impact on sewer denitrification kinetic profile, as it determines the extent of temporal nitrite accumulation. The temperature coefficient of each anoxic process, including sulfide oxidation, nitrate utilization and denitrification/nitrite utilization is experimentally calculated and temperature dependent equations are developed, providing the rate of all anoxic processes in bulk phase of sewer wastewater, in any given temperature.

Community Composition of Nitrous Oxide Consuming Bacteria in the Oxygen Minimum Zone of the Eastern Tropical South Pacific

PubMed Central

Sun, Xin; Jayakumar, Amal; Ward, Bess B.

2017-01-01

The ozone-depleting and greenhouse gas, nitrous oxide (N2O), is mainly consumed by the microbially mediated anaerobic process, denitrification. N2O consumption is the last step in canonical denitrification, and is also the least O2 tolerant step. Community composition of total and active N2O consuming bacteria was analyzed based on total (DNA) and transcriptionally active (RNA) nitrous oxide reductase (nosZ) genes using a functional gene microarray. The total and active nosZ communities were dominated by a limited number of nosZ archetypes, affiliated with bacteria from marine, soil and marsh environments. In addition to nosZ genes related to those of known marine denitrifiers, atypical nosZ genes, related to those of soil bacteria that do not possess a complete denitrification pathway, were also detected, especially in surface waters. The community composition of the total nosZ assemblage was significantly different from the active assemblage. The community composition of the total nosZ assemblage was significantly different between coastal and off-shore stations. The low oxygen assemblages from both stations were similar to each other, while the higher oxygen assemblages were more variable. Community composition of the active nosZ assemblage was also significantly different between stations, and varied with N2O concentration but not O2. Notably, nosZ assemblages were not only present but also active in oxygenated seawater: the abundance of total and active nosZ bacteria from oxygenated surface water (indicated by nosZ gene copy number) was similar to or even larger than in anoxic waters, implying the potential for N2O consumption even in the oxygenated surface water. PMID:28702012

Community Composition of Nitrous Oxide Consuming Bacteria in the Oxygen Minimum Zone of the Eastern Tropical South Pacific.

PubMed

Sun, Xin; Jayakumar, Amal; Ward, Bess B

2017-01-01

The ozone-depleting and greenhouse gas, nitrous oxide (N 2 O), is mainly consumed by the microbially mediated anaerobic process, denitrification. N 2 O consumption is the last step in canonical denitrification, and is also the least O 2 tolerant step. Community composition of total and active N 2 O consuming bacteria was analyzed based on total (DNA) and transcriptionally active (RNA) nitrous oxide reductase ( nosZ ) genes using a functional gene microarray. The total and active nosZ communities were dominated by a limited number of nosZ archetypes, affiliated with bacteria from marine, soil and marsh environments. In addition to nosZ genes related to those of known marine denitrifiers, atypical nosZ genes, related to those of soil bacteria that do not possess a complete denitrification pathway, were also detected, especially in surface waters. The community composition of the total nosZ assemblage was significantly different from the active assemblage. The community composition of the total nosZ assemblage was significantly different between coastal and off-shore stations. The low oxygen assemblages from both stations were similar to each other, while the higher oxygen assemblages were more variable. Community composition of the active nosZ assemblage was also significantly different between stations, and varied with N 2 O concentration but not O 2 . Notably, nosZ assemblages were not only present but also active in oxygenated seawater: the abundance of total and active nosZ bacteria from oxygenated surface water (indicated by nosZ gene copy number) was similar to or even larger than in anoxic waters, implying the potential for N 2 O consumption even in the oxygenated surface water.

Nitrous oxide from aerated dairy manure slurries: Effects of aeration rates and oxic/anoxic phasing.

PubMed

Molodovskaya, Marina; Singurindy, Olga; Richards, Brian K; Steenhuis, Tammo S

2008-12-01

Small-scale laboratory research was conducted to compare the effects of different aeration rates and oxic/anoxic phasing on nitrous oxide (N(2)O) formation from dairy manure slurries. Manure slurry samples were incubated in triplicate for three-weeks under a range of continuous sweep gas flows (0.01-0.23L min(-1)kg(-1) slurry) with and without oxygen (air and dinitrogen gas). The net release of N(2)O-N was affected by both aeration rates and oxic/anoxic conditions, whereas ammonia volatilization depended mainly on gas flow rates. Maximum N(2)O-N losses after three-weeks incubation were 4.2% of total slurry N. Major N losses (up to 50% of total slurry N) were caused by ammonia volatilization that increased with increasing gas flow rates. The lowest nitrous oxide and ammonia production was observed from low flow phased oxic/anoxic treatment.

Multiresistant opportunistic pathogenic bacteria isolated from polluted rivers and first detection of nontuberculous mycobacteria in the Algerian aquatic environment.

PubMed

Djouadi, Lydia Neïla; Selama, Okba; Abderrahmani, Ahmed; Bouanane-Darenfed, Amel; Abdellaziz, Lamia; Amziane, Meriam; Fardeau, Marie-Laure; Nateche, Farida

2017-08-01

Opportunistic infections constitute a major challenge for modern medicine mainly because the involved bacteria are usually multiresistant to antibiotics. Most of these bacteria possess remarkable ability to adapt to various ecosystems, including those exposed to anthropogenic activities. This study isolated and identified 21 multiresistant opportunistic bacteria from two polluted rivers, located in Algiers. Cadmium, lead, and copper concentrations were determined for both water samples to evaluate heavy metal pollution. High prevalence of Enterobacteria and non-fermentative Gram-negative rods was found and a nontuberculous Mycobacterium (NTM) strain was isolated. To the best of our knowledge, this is the first detection of NTM in the Algerian environment. The strains were tested for their resistance against 34 antibiotics and 8 heavy metals. Multiple antibiotics and heavy metals resistance was observed in all isolates. The two most resistant strains, identified as Acinetobacter sp. and Citrobacter freundii, were submitted to plasmid curing to determine if resistance genes were plasmid or chromosome encoded. Citrobacter freundii strain P18 showed a high molecular weight plasmid which seems to code for resistance to zinc, lead, and tetracycline, at the same time. These findings strongly suggest that anthropized environments constitute a reservoir for multiresistant opportunistic bacteria and for circulating resistance genes.

Uranium isotope evidence for two episodes of deoxygenation during Oceanic Anoxic Event 2

NASA Astrophysics Data System (ADS)

Clarkson, Matthew O.; Stirling, Claudine H.; Jenkyns, Hugh C.; Dickson, Alexander J.; Porcelli, Don; Moy, Christopher M.; Pogge von Strandmann, Philip A. E.; Cooke, Ilsa R.; Lenton, Timothy M.

2018-03-01

Oceanic Anoxic Event 2 (OAE 2), occurring ˜94 million years ago, was one of the most extreme carbon cycle and climatic perturbations of the Phanerozoic Eon. It was typified by a rapid rise in atmospheric CO2, global warming, and marine anoxia, leading to the widespread devastation of marine ecosystems. However, the precise timing and extent to which oceanic anoxic conditions expanded during OAE 2 remains unresolved. We present a record of global ocean redox changes during OAE 2 using a combined geochemical and carbon cycle modeling approach. We utilize a continuous, high-resolution record of uranium isotopes in pelagic and platform carbonate sediments to quantify the global extent of seafloor anoxia during OAE 2. This dataset is then compared with a dynamic model of the coupled global carbon, phosphorus, and uranium cycles to test hypotheses for OAE 2 initiation. This unique approach highlights an intra-OAE complexity that has previously been underconstrained, characterized by two expansions of anoxia separated by an episode of globally significant reoxygenation coincident with the “Plenus Cold Event.” Each anoxic expansion event was likely driven by rapid atmospheric CO2 injections from multiphase Large Igneous Province activity.

Incineration of tannery sludge under oxic and anoxic conditions: study of chromium speciation.

PubMed

Kavouras, P; Pantazopoulou, E; Varitis, S; Vourlias, G; Chrissafis, K; Dimitrakopulos, G P; Mitrakas, M; Zouboulis, A I; Karakostas, Th; Xenidis, A

2015-01-01

A tannery sludge, produced from physico-chemical treatment of tannery wastewaters, was incinerated without any pre-treatment process under oxic and anoxic conditions, by controlling the abundance of oxygen. Incineration in oxic conditions was performed at the temperature range from 300°C to 1200°C for duration of 2h, while in anoxic conditions at the temperature range from 400°C to 600°C and varying durations. Incineration under oxic conditions at 500°C resulted in almost total oxidation of Cr(III) to Cr(VI), with CaCrO4 to be the crystalline phase containing Cr(VI). At higher temperatures a part of Cr(VI) was reduced, mainly due to the formation of MgCr2O4. At 1200°C approximately 30% of Cr(VI) was reduced to Cr(III). Incineration under anoxic conditions substantially reduced the extent of oxidation of Cr(III) to Cr(VI). Increase of temperature and duration of incineration lead to increase of Cr(VI) content, while no chromium containing crystalline phase was detected. Copyright © 2014 Elsevier B.V. All rights reserved.

ENANTIOSELECTIVE MICROBIAL TRANSFORMATION OF THE PHENYLPYRAZOLE INSECTICIDE FIPRONIL IN ANOXIC SEDIMENTS

EPA Science Inventory

Fipronil, a chiral insecticide, was biotransformed initially to fipronil sulfide in anoxic sediment slurries following a short lag period. Sediment slurries characterized as either sulfidogenic or methanogenic transformed fipronil with half-lives of approximately 35 and 40 days, ...

Improving diversity in cultures of bacteria from an extreme environment.

PubMed

Vester, Jan Kjølhede; Glaring, Mikkel Andreas; Stougaard, Peter

2013-08-01

The ikaite columns in the Ikka Fjord in Greenland represent one of the few permanently cold and alkaline environments on Earth, and the interior of the columns is home to a bacterial community adapted to these extreme conditions. The community is characterized by low cell numbers imbedded in a calcium carbonate matrix, making extraction of bacterial cells and DNA a challenge and limiting molecular and genomic studies of this environment. To utilize this genetic resource, cultivation at high pH and low temperature was studied as a method for obtaining biomass and DNA from the fraction of this community that would not otherwise be amenable to genetic analyses. The diversity and community dynamics in mixed cultures of bacteria from ikaite columns was investigated using denaturing gradient gel electrophoresis and pyrosequencing of 16S rDNA. Both medium composition and incubation time influenced the diversity of the culture and many hitherto uncharacterized genera could be brought into culture by extended incubation time. Extended incubation time also gave rise to a more diverse community with a significant number of rare species not detected in the initial community.

Multilocus sequence analysis for assessment of phylogenetic diversity and biogeography in Thalassospira bacteria from diverse marine environments.

PubMed

Lai, Qiliang; Liu, Yang; Yuan, Jun; Du, Juan; Wang, Liping; Sun, Fengqin; Shao, Zongze

2014-01-01

Thalassospira bacteria are widespread and have been isolated from various marine environments. Less is known about their genetic diversity and biogeography, as well as their role in marine environments, many of them cannot be discriminated merely using the 16S rRNA gene. To address these issues, in this report, the phylogenetic analysis of 58 strains from seawater and deep sea sediments were carried out using the multilocus sequence analysis (MLSA) based on acsA, aroE, gyrB, mutL, rpoD and trpB genes, and the DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) based on genome sequences. The MLSA analysis demonstrated that the 58 strains were clearly separated into 15 lineages, corresponding to seven validly described species and eight potential novel species. The DDH and ANI values further confirmed the validity of the MLSA analysis and eight potential novel species. The MLSA interspecies gap of the genus Thalassospira was determined to be 96.16-97.12% sequence identity on the basis of the combined analyses of the DDH and MLSA, while the ANIm interspecies gap was 95.76-97.20% based on the in silico DDH analysis. Meanwhile, phylogenetic analyses showed that the Thalassospira bacteria exhibited distribution pattern to a certain degree according to geographic regions. Moreover, they clustered together according to the habitats depth. For short, the phylogenetic analyses and biogeography of the Thalassospira bacteria were systematically investigated for the first time. These results will be helpful to explore further their ecological role and adaptive evolution in marine environments.

Multilocus Sequence Analysis for Assessment of Phylogenetic Diversity and Biogeography in Thalassospira Bacteria from Diverse Marine Environments

PubMed Central

Yuan, Jun; Du, Juan; Wang, Liping; Sun, Fengqin; Shao, Zongze

2014-01-01

Thalassospira bacteria are widespread and have been isolated from various marine environments. Less is known about their genetic diversity and biogeography, as well as their role in marine environments, many of them cannot be discriminated merely using the 16S rRNA gene. To address these issues, in this report, the phylogenetic analysis of 58 strains from seawater and deep sea sediments were carried out using the multilocus sequence analysis (MLSA) based on acsA, aroE, gyrB, mutL, rpoD and trpB genes, and the DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) based on genome sequences. The MLSA analysis demonstrated that the 58 strains were clearly separated into 15 lineages, corresponding to seven validly described species and eight potential novel species. The DDH and ANI values further confirmed the validity of the MLSA analysis and eight potential novel species. The MLSA interspecies gap of the genus Thalassospira was determined to be 96.16–97.12% sequence identity on the basis of the combined analyses of the DDH and MLSA, while the ANIm interspecies gap was 95.76–97.20% based on the in silico DDH analysis. Meanwhile, phylogenetic analyses showed that the Thalassospira bacteria exhibited distribution pattern to a certain degree according to geographic regions. Moreover, they clustered together according to the habitats depth. For short, the phylogenetic analyses and biogeography of the Thalassospira bacteria were systematically investigated for the first time. These results will be helpful to explore further their ecological role and adaptive evolution in marine environments. PMID:25198177

Oxygenic and anoxygenic photosynthesis in a microbial mat from an anoxic and sulfidic spring.

PubMed

de Beer, Dirk; Weber, Miriam; Chennu, Arjun; Hamilton, Trinity; Lott, Christian; Macalady, Jennifer; M Klatt, Judith

2017-03-01

Oxygenic and anoxygenic photosynthesis were studied with microsensors in microbial mats found at 9-10 m depth in anoxic and sulfidic water in Little Salt Spring (Florida, USA). The lake sediments were covered with a 1-2 mm thick red mat dominated by filamentous Cyanobacteria, below which Green Sulfur Bacteria (GSB, Chlorobiaceae) were highly abundant. Within 4 mm inside the mats, the incident radiation was attenuated to undetectable levels. In situ microsensor data showed both oxygenic photosynthesis in the red surface layer and light-induced sulfide dynamics up to 1 cm depth. Anoxygenic photosynthesis occurred during all daylight hours, with complete sulfide depletion around midday. Oxygenic photosynthesis was limited to 4 h per day, due to sulfide inhibition in the early morning and late afternoon. Laboratory measurements on retrieved samples showed that oxygenic photosynthesis was fully but reversibly inhibited by sulfide. In patches Fe(III) alleviated the inhibition of oxygenic photosynthesis by sulfide. GSB were resistant to oxygen and showed a low affinity to sulfide. Their light response showed saturation at very low intensities. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Remote-controlled robotic platform ORPHEUS as a new tool for detection of bacteria in the environment.

PubMed

Nejdl, Lukas; Kudr, Jiri; Cihalova, Kristyna; Chudobova, Dagmar; Zurek, Michal; Zalud, Ludek; Kopecny, Lukas; Burian, Frantisek; Ruttkay-Nedecky, Branislav; Krizkova, Sona; Konecna, Marie; Hynek, David; Kopel, Pavel; Prasek, Jan; Adam, Vojtech; Kizek, Rene

2014-08-01

Remote-controlled robotic systems are being used for analysis of various types of analytes in hostile environment including those called extraterrestrial. The aim of our study was to develop a remote-controlled robotic platform (ORPHEUS-HOPE) for bacterial detection. For the platform ORPHEUS-HOPE a 3D printed flow chip was designed and created with a culture chamber with volume 600 μL. The flow rate was optimized to 500 μL/min. The chip was tested primarily for detection of 1-naphthol by differential pulse voltammetry with detection limit (S/N = 3) as 20 nM. Further, the way how to capture bacteria was optimized. To capture bacterial cells (Staphylococcus aureus), maghemite nanoparticles (1 mg/mL) were prepared and modified with collagen, glucose, graphene, gold, hyaluronic acid, and graphene with gold or graphene with glucose (20 mg/mL). The most up to 50% of the bacteria were captured by graphene nanoparticles modified with glucose. The detection limit of the whole assay, which included capturing of bacteria and their detection under remote control operation, was estimated as 30 bacteria per μL. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biocalcification by halophilic bacteria for remediation of concrete structures in marine environment.

PubMed

Bansal, Roohi; Dhami, Navdeep Kaur; Mukherjee, Abhijit; Reddy, M Sudhakara

2016-11-01

Microbial carbonate precipitation has emerged as a promising technology for remediation and restoration of concrete structures. Deterioration of reinforced concrete structures in marine environments is a major concern due to chloride-induced corrosion. In the current study, halophilic bacteria Exiguobacterium mexicanum was isolated from sea water and tested for biomineralization potential under different salt stress conditions. The growth, urease and carbonic anhydrase production significantly increased under salt stress conditions. Maximum calcium carbonate precipitation was recorded at 5 % NaCl concentration. Application of E. mexicanum on concrete specimens significantly increased the compressive strength (23.5 %) and reduced water absorption about five times under 5 % salt stress conditions compared to control specimens. SEM and XRD analysis of bacterial-treated concrete specimens confirmed the precipitation of calcite. The present study results support the potential of this technology for improving the strength and durability properties of building structures in marine environments.

Enhanced biological nutrient removal in sequencing batch reactors operated as static/oxic/anoxic (SOA) process.

PubMed

Xu, Dechao; Chen, Hongbo; Li, Xiaoming; Yang, Qi; Zeng, Tianjing; Luo, Kun; Zeng, Guangming

2013-09-01

An innovative static/oxic/anoxic (SOA) activated sludge process characterized by static phase as a substitute for conventional anaerobic stage was developed to enhance biological nutrient removal (BNR) with influent ammonia of 20 and 40 mg/L in R1 and R2 reactors, respectively. The results demonstrated that static phase could function as conventional anaerobic stage. In R1 lower influent ammonia concentration facilitated more polyphosphate accumulating organisms (PAOs) growth, but secondary phosphorus release occurred due to NOx(-) depletion during post-anoxic period. In R2, however, denitrifying phosphorus removal proceeded with sufficient NOx(-). Both R1 and R2 saw simultaneous nitrification-denitrification. Glycogen was utilized to drive post-denitrification with denitrification rates in excess of typical endogenous decay rates. The anoxic stirring duration could be shortened from 3 to 1.5h to avoid secondary phosphorus release in R1 and little adverse impact was found on nutrients removal in R2. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bacteria-mediated bisphenol A degradation.

PubMed

Zhang, Weiwei; Yin, Kun; Chen, Lingxin

2013-07-01

Bisphenol A (BPA) is an important monomer in the manufacture of polycarbonate plastics, food cans, and other daily used chemicals. Daily and worldwide usage of BPA and BPA-contained products led to its ubiquitous distribution in water, sediment/soil, and atmosphere. Moreover, BPA has been identified as an environmental endocrine disruptor for its estrogenic and genotoxic activity. Thus, BPA contamination in the environment is an increasingly worldwide concern, and methods to efficiently remove BPA from the environment are urgently recommended. Although many factors affect the fate of BPA in the environment, BPA degradation is mainly depended on the metabolism of bacteria. Many BPA-degrading bacteria have been identified from water, sediment/soil, and wastewater treatment plants. Metabolic pathways of BPA degradation in specific bacterial strains were proposed, based on the metabolic intermediates detected during the degradation process. In this review, the BPA-degrading bacteria were summarized, and the (proposed) BPA degradation pathway mediated by bacteria were referred.

Nitrogen and phosphorus removal in pilot-scale anaerobic-anoxic oxidation ditch system.

PubMed

Peng, Yongzhen; Hou, Hongxun; Wang, Shuying; Cui, Youwei; Zhiguo, Yuan

2008-01-01

To achieve high efficiency of nitrogen and phosphorus removal and to investigate the rule of simultaneous nitrification and denitrification phosphorus removal (SNDPR), a whole course of SNDPR damage and recovery was studied in a pilot-scale, anaerobic-anoxic oxidation ditch (OD), where the volumes of anaerobic zone, anoxic zone, and ditches zone of the OD system were 7, 21, and 280 L, respectively. The reactor was fed with municipal wastewater with a flow rate of 336 L/d. The concept of simultaneous nitrification and denitrification (SND) rate (r(SND)) was put forward to quantify SND. The results indicate that: (1) high nitrogen and phosphorus removal efficiencies were achieved during the stable SND phase, total nitrogen (TN) and total phosphate (TP) removal rates were 80% and 85%, respectively; (2) when the system was aerated excessively, the stability of SND was damaged, and r(SND) dropped from 80% to 20% or less; (3) the natural logarithm of the ratio of NO(x) to NH4+ in the effluent had a linear correlation to oxidation-reduction potential (ORP); (4) when NO3- was less than 6 mg/L, high phosphorus removal efficiency could be achieved; (5) denitrifying phosphorus removal (DNPR) could take place in the anaerobic-anoxic OD system. The major innovation was that the SND rate was devised and quantified.

Bacterial Communities of Three Saline Meromictic Lakes in Central Asia.

PubMed

Baatar, Bayanmunkh; Chiang, Pei-Wen; Rogozin, Denis Yu; Wu, Yu-Ting; Tseng, Ching-Hung; Yang, Cheng-Yu; Chiu, Hsiu-Hui; Oyuntsetseg, Bolormaa; Degermendzhy, Andrey G; Tang, Sen-Lin

2016-01-01

Meromictic lakes located in landlocked steppes of central Asia (~2500 km inland) have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon) in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Firmicutes were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, Thiocapsa and Halochromatium) were predominant bacterial components in the anoxic layer of Lake Shira (~20.6% of relative abundance), Lake Shunet (~27.1%) and Lake Oigon (~9.25%), respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12%) in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H2S and salinity) were associated (P< 0.05) with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches.

Bacterial Communities of Three Saline Meromictic Lakes in Central Asia

PubMed Central

Baatar, Bayanmunkh; Chiang, Pei-Wen; Rogozin, Denis Yu; Wu, Yu-Ting; Tseng, Ching-Hung; Yang, Cheng-Yu; Chiu, Hsiu-Hui; Oyuntsetseg, Bolormaa; Degermendzhy, Andrey G.; Tang, Sen-Lin

2016-01-01

Meromictic lakes located in landlocked steppes of central Asia (~2500 km inland) have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon) in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Firmicutes were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, Thiocapsa and Halochromatium) were predominant bacterial components in the anoxic layer of Lake Shira (~20.6% of relative abundance), Lake Shunet (~27.1%) and Lake Oigon (~9.25%), respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12%) in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H2S and salinity) were associated (P< 0.05) with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches. PMID:26934492

Present-day biogeochemical activities of anaerobic bacteria and their relevance to future exobiological investigations

USGS Publications Warehouse

Oremland, R.S.

1989-01-01

If the primordial atmosphere was reducing, then the first microbial ecosystem was probably composed of anaerobic bacteria. However, despite the presence of an oxygen-rich atmosphere, anaerobic habitats are important, commonplace components of the Earth's present biosphere. The geochemical activities displayed by these anaerobes impact the global cycling of certain elements (e.g., C, N, S, Fe, Mn, etc.). Methane provides an obvious example of how human-enhanced activities on a global scale can influence the content of a "radiative" (i.e., infrared absorbing) trace gas in the atmosphere. Methane can be oxidized by anaerobic bacteria, but this does not appear to support their growth. Acetylene, however, does support such growth. This may form the basis for future exobiological investigations of the atmospheres of anoxic, hydrocarbon-rich planets like Jupiter and Saturn, as well as the latter's satellite Titan. ?? 1989.

The early Toarcian anoxic event: what the beginning and the end of the story are?

NASA Astrophysics Data System (ADS)

Mattioli, Emanuela; Plancq, Julien; Raucsik, Béla

2010-05-01

very high, and assemblages seem not to record an environmental stress. The study of the calcareous nannofossil assemblages along a W-E transect in the NW-Tethyan shelf shows a progressive, but significant decrease in abundance fluxes from W to E, and the lowest fluxes are recorded in the Mecsek Basin that was closer to the oceanic Tethys. A progressive re-colonization of the lower photic zone by deep-dweller nannofossil taxa, mainly Crepidolithus crassus, is observed in the aftermath of the anoxic event, but this re-colonization occurred earlier in the Mecsek Basin, probably because of more effective marine connections with the open-ocean. This set of data indicates that: (1) environmental deterioration was recurrent until it reached its acme during the T-OAE; (2) post-crisis recovery of surface water environments was not synchronous, depending on palaeoceanographic conditions occurring within the western Tethys. Our scenario implies an intrinsically long-lasting suite of events and argues in favour of long-lasting CO2 degassing, most likely related to the emplacement of the large igneous province of Karoo-Ferrar as the main cause of the Toarcian environmental perturbations. Acknowledgements. We would like to thank John McArthur for kindly providing us the Toarcian samples from the Yorkshire coast. Hesselbo et al. (2007). Carbon-isotope record of the Early Jurassic (Toarcian) oceanic anoxic event from fossil wood and marine carbonate (Lusitanian Basin, Portugal), Earth Planet. Sci. Lett. 253, 455- 470. Mattioli et al. (2008). Calcareous nannoplankton changes across the early Toarcian oceanic anoxic event in the western Tethys. Paleoceanography 23, PA3208, doi:10.1029/2007PA001435, 2008. Suan et al. (2008a). Duration of the Early Toarcian carbon isotope excursion deduced from spectral analysis: Consequence for its possible causes. Earth Planet. Sci. Lett. 267, 666-679. Suan et al. (2008b). Evidence for major environmental perturbation prior to and during the Toarcian

Reduction of elemental selenium to selenide: Experiments with anoxic sediments and bacteria that respire Se-oxyanions

USGS Publications Warehouse

Herbel, M.J.; Blum, J.S.; Oremland, R.S.; Borglin, S.E.

2003-01-01

A selenite-respiring bacterium, Bacillus selenitireducens, produced significant levels of Se(-II) (as aqueous HSe-) when supplied with Se(O). B. selenitireducens was also able to reduce selenite [Se(IV)] through Se(O) to Se(-II). Reduction of Se(O) by B.selenitireducens was more rapid in cells grown on colloidal sulfur [S(O)] or Se(IV) as their electron acceptor than for cell lines grown on fumarate. In contrast, three cultures of selenate-respiring bacteria, Sulfurospirillum barnesii, B. arsenicoselenatis, and Selenihalanaerobacter shriftii either were unable to reduce Se(O) to Se(-II) or had only a very limited capacity to achieve this reduction. Biological reduction of Se(O) to Se(-II) was observed during incubation of estuarine sediment slurries, while no such activity was noted in formalin-killed controls. The majority of the Se(-II) produced was found in the sediments as a solid precipitate of FeSe, rather than in solution as HSe-. These results demonstrate that certain anaerobic bacteria have the capacity to reduce Se(O) to Se(-II), providing a possible biological explanation for the occurrence of the selenide species in some sedimentary rocks.

Influence of microorganisms on the oxidation state distribution of multivalent actinides under anoxic conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reed, Donald Timothy; Borkowski, Marian; Lucchini, Jean - Francois

2010-12-10

The fate and potential mobility of multivalent actinides in the subsurface is receiving increased attention as the DOE looks to cleanup the many legacy nuclear waste sites and associated subsurface contamination. Plutonium, uranium and neptunium are the near-surface multivalent contaminants of concern and are also key contaminants for the deep geologic disposal of nuclear waste. Their mobility is highly dependent on their redox distribution at their contamination source as well as along their potential migration pathways. This redox distribution is often controlled, especially in the near-surface where organic/inorganic contaminants often coexist, by the direct and indirect effects of microbial activity.more » Under anoxic conditions, indirect and direct bioreduction mechanisms exist that promote the prevalence of lower-valent species for multivalent actinides. Oxidation-state-specific biosorption is also an important consideration for long-term migration and can influence oxidation state distribution. Results of ongoing studies to explore and establish the oxidation-state specific interactions of soil bacteria (metal reducers and sulfate reducers) as well as halo-tolerant bacteria and Archaea for uranium, neptunium and plutonium will be presented. Enzymatic reduction is a key process in the bioreduction of plutonium and uranium, but co-enzymatic processes predominate in neptunium systems. Strong sorptive interactions can occur for most actinide oxidation states but are likely a factor in the stabilization of lower-valent species when more than one oxidation state can persist under anaerobic microbiologically-active conditions. These results for microbiologically active systems are interpreted in the context of their overall importance in defining the potential migration of multivalent actinides in the subsurface.« less

Effect of gas-liquid flow pattern and microbial diversity analysis of a pilot-scale biotrickling filter for anoxic biogas desulfurization.

PubMed

Almenglo, Fernando; Bezerra, Tercia; Lafuente, Javier; Gabriel, David; Ramírez, Martín; Cantero, Domingo

2016-08-01

Hydrogen sulfide removal from biogas was studied under anoxic conditions in a pilot-scale biotrickling filter operated under counter- and co-current gas-liquid flow patterns. The best performance was found under counter-current conditions (maximum elimination capacity of 140 gS m(-3) h(-1)). Nevertheless, switching conditions between co- and counter-current flow lead to a favorable redistribution of biomass and elemental sulfur along the bed height. Moreover, elemental sulfur was oxidized to sulfate when the feeding biogas was disconnected and the supply of nitrate (electron acceptor) was maintained. Removal of elemental sulfur was important to prevent clogging in the packed bed and, thereby, to increase the lifespan of the packed bed between maintenance episodes. The larger elemental sulfur removal rate during shutdowns was 59.1 gS m(-3) h(-1). Tag-encoded FLX amplicon pyrosequencing was used to study the diversity of bacteria under co-current flow pattern with liquid recirculation and counter-current mode with a single-pass flow of the liquid phase. The main desulfurizing bacteria were Sedimenticola while significant role of heterotrophic, opportunistic species was envisaged. Remarkable differences between communities were found when a single-pass flow of industrial water was fed to the biotrickling filter. Copyright © 2016 Elsevier Ltd. All rights reserved.

Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column.

PubMed

Bertagnolli, Anthony D; Padilla, Cory C; Glass, Jennifer B; Thamdrup, Bo; Stewart, Frank J

2017-11-01

Marinimicrobia bacteria are widespread in subeuphotic areas of the oceans and particularly abundant in oxygen minimum zones (OMZs). Information on Marinimicrobia metabolism is sparse, making the biogeochemical influence of this group challenging to predict. Here, metagenome-assembled genomes representing Marinimicrobia subgroups PN262000N21 and ARCTIC96B-7 were retrieved to near completion (97% and 94%) from OMZ metagenomes, with contamination (14.1%) observed only in ARCTIC96B-7. Genes for aerobic carbon monoxide (CO) oxidation, polysulfide metabolism and hydrogen utilization were identified only in PN262000N21, while genes for partial denitrification occurred in both genomes. Transcripts mapping to these genomes increased from <0.3% of total mRNA from the oxic zone to a max of 22% under anoxia. ARCTIC96B-7 transcript representation decreased an order of magnitude from non-sulfidic to sulfidic depths. In contrast, PN262000N21 representation was relatively constant throughout the OMZ, although transcripts encoding sulfur-utilizing proteins, including sulfur transferases, were enriched at sulfidic depths. PN262000N21 transcripts encoding a protein with fibronectin domains similar to those in cellulosome-producing bacteria were also abundant, suggesting a potential for high molecular weight carbon cycling. These data provide omic-level descriptions of metabolic potential and activity in OMZ-associated Marinimicrobia, suggesting differentiation between subgroups with roles in carbon and dissimilatory inorganic nitrogen and sulfur cycling. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Constraining the rate of oceanic deoxygenation leading up to a Cretaceous Oceanic Anoxic Event (OAE-2: ~94 Ma)

PubMed Central

Ostrander, Chadlin M.; Owens, Jeremy D.; Nielsen, Sune G.

2017-01-01

The rates of marine deoxygenation leading to Cretaceous Oceanic Anoxic Events are poorly recognized and constrained. If increases in primary productivity are the primary driver of these episodes, progressive oxygen loss from global waters should predate enhanced carbon burial in underlying sediments—the diagnostic Oceanic Anoxic Event relic. Thallium isotope analysis of organic-rich black shales from Demerara Rise across Oceanic Anoxic Event 2 reveals evidence of expanded sediment-water interface deoxygenation ~43 ± 11 thousand years before the globally recognized carbon cycle perturbation. This evidence for rapid oxygen loss leading to an extreme ancient climatic event has timely implications for the modern ocean, which is already experiencing large-scale deoxygenation. PMID:28808684

Okenane, a biomarker for purple sulfur bacteria (Chromatiaceae), and other new carotenoid derivatives from the 1640 Ma Barney Creek Formation

NASA Astrophysics Data System (ADS)

Brocks, Jochen J.; Schaeffer, Philippe

2008-03-01

Carbonates of the 1640 million years (Ma) old Barney Creek Formation (BCF), McArthur Basin, Australia, contain more than 22 different C 40 carotenoid derivatives including lycopane, γ-carotane, β-carotane, chlorobactane, isorenieratane, β-isorenieratane, renieratane, β-renierapurpurane, renierapurpurane and the monoaromatic carotenoid okenane. These biomarkers extend the geological record of carotenoid derivatives by more than 1000 million years. Okenane is potentially derived from the red-colored aromatic carotenoid okenone. Based on a detailed review of the ecology and physiology of all extant species that are known to contain okenone, we interpret fossil okenane as a biomarker for planktonic purple sulfur bacteria of the family Chromatiaceae. Okenane is strictly a biomarker for anoxic and sulfidic conditions in the presence of light (photic zone euxinia) and indicates an anoxic/oxic transition (temporarily) located at less than 25 m depth and, with a high probability, less than 12 m depth. For the BCF, we also interpret renierapurpurane, renieratane and β-renierapurpurane as biomarkers for Chromatiaceae with a possible contribution of cyanobacterial synechoxanthin to the renierapurpurane pool. Although isorenieratane may, in principle, be derived from actinobacteria, in the BCF these biomarkers almost certainly derive from sulfide-oxidizing phototrophic green sulfur bacteria (Chlorobiaceae). Biological precursors of γ-carotane, β-carotane and lycopane are found among numerous autotrophic and almost all phototrophic organisms in the three domains of life. In the BCF, a paucity of diagnostic eukaryotic steroids suggests that algae were rare and, therefore, that cyanobacterial carotenoids such as β-carotene, echinenone, canthaxanthin and zeaxanthin are the most likely source of observed β-carotane. γ-Carotane may be derived from cyanobacteria, Chlorobiaceae and green non-sulfur bacteria (Chloroflexi), while the most likely biological sources for lycopane

Bacteria mediated dissolution of pyromorphite Pb5(PO4)3Cl in presence of Pseudomonas putida bacteria - an effect on Pb remobilization in the environment

NASA Astrophysics Data System (ADS)

Flis, Justyna; Manecki, Maciej; Merkel, Broder J.; Latowski, Dariusz

2010-05-01

The objective of the study was to determine the mechanisms of microbially enhanced dissolution of lead phosphate-pyromorphite Pb5(PO4)3Cl). Contrary to the current literature, the results of our experiments indicate a great potential for Pb remobilization in the environment by an aerobic microorganism acquiring phosphates. Broad knowledge exists about the role of Pb-apatites in regulating the behavior and the bioavailability of Pb in soils and wastewater. In situ Pb immobilization is one of the methods now routinely applied for the reclamation of Pb-contaminated soils, including shallow unconfined aquifers (Magalhaes & Silva, 2003; Magalhaes, 2002; Ma et al. 1993). This method is based on the principle that aqueous phosphates added to soil pore solutions form a very stable (insoluble) mineral pyromorphite (Pb-apatite) Pb5(PO4)3Cl. Bioavailability of aqueous Pb is thus minimized due to the very low solubility and the high thermodynamic stability of pyromorphite (Flis, 2007; Nriagu, 1974). Several reports have examined the ability of different bacterial species including Pseudomonas to solubilise insoluble inorganic phosphate compounds for example apatites (Welch et al., 2002; Maurice et al., 1999; Rodriguez and Fraga, 1999 ). Various species of Pseudomonas genera are encountered as common inhabitants of soils and wastes in the industrial areas under strong pollution influence. To date, there has not been any published evidence of microbial dissolution of pyromorphite. The major objective of the project was to study Pseudomonas putida growth in the presence of Pb-apatite (Pb5(PO4)3Cl) as the sole source of phosphate. It was to test the hypothesis that in the phosphate deficient environment bacteria are able to actively scavenge for P from the Pb-apatite which results in remobilization of Pb in the environment. The bacteria growth was investigated at 22oC. Commercially available Pseudomonas putida strain was used throughout. The experiment and its controls were run in

Disproportionation of elemental sulfur by haloalkaliphilic bacteria from soda lakes.

PubMed

Poser, Alexander; Lohmayer, Regina; Vogt, Carsten; Knoeller, Kay; Planer-Friedrich, Britta; Sorokin, Dimitry; Richnow, Hans-H; Finster, Kai

2013-11-01

Microbial disproportionation of elemental sulfur to sulfide and sulfate is a poorly characterized part of the anoxic sulfur cycle. So far, only a few bacterial strains have been described that can couple this reaction to cell growth. Continuous removal of the produced sulfide, for instance by oxidation and/or precipitation with metal ions such as iron, is essential to keep the reaction exergonic. Hitherto, the process has exclusively been reported for neutrophilic anaerobic bacteria. Here, we report for the first time disproportionation of elemental sulfur by three pure cultures of haloalkaliphilic bacteria isolated from soda lakes: the Deltaproteobacteria Desulfurivibrio alkaliphilus and Desulfurivibrio sp. AMeS2, and a member of the Clostridia, Dethiobacter alkaliphilus. All cultures grew in saline media at pH 10 by sulfur disproportionation in the absence of metals as sulfide scavengers. Our data indicate that polysulfides are the dominant sulfur species under highly alkaline conditions and that they might be disproportionated. Furthermore, we report the first organism (Dt. alkaliphilus) from the class Clostridia that is able to grow by sulfur disproportionation.

Jurassic carbonate microfacies, sea-level changes and the Toarcian anoxic event in the Tethys Himalaya (South Tibet)

NASA Astrophysics Data System (ADS)

Han, Zhong; Hu, Xiumian; Garzanti, Eduardo

2016-04-01

Detailed microfacies analysis of carbonate rocks from the Tingri and Nyalam areas of South Tibet allowed us to reconstruct the evolution of sedimentary environments during the Early to Middle Jurassic. Based on texture, sedimentary structure, grain composition and fossil content of about 500 thin sections, 17 microfacies overall were identified, and three evolutionary stages were defined. Stage 1 (Rhaetian?-lower Sinemurian Zhamure Formation) was characterized by siliciclastic and mixed siliciclastic-carbonate sedimentation on a barrier shore environment, stage 2 (upper Sinemurian-Pliensbachian Pupuga Formation) by high-energy grainstones with rich benthic faunas thriving on a carbonate platform, and stage 3 (Toarcian-lower Bajocian Nieniexiongla Formation) by low-energy mudstones intercalated with frequent storm layers on a carbonate ramp. Besides, Carbon isotope analyses (δ13Ccarb and δ13Corg) were performed on the late Pliensbachian-early Toarcian interval, and the organic matter recorded a pronounced stepped negative excursion -4.5‰ corresponding to characteristics of the early Toarcian oceanic anoxic event globally, which began just below the stage 2-stage 3 facies shifting boundary. The comparison between the Tethys Himalaya (South Tibet) and the tropical/subtropical zones of the Western Tethys and Panthalassa was carried out to discuss the factors controlling sedimentary evolution. The change from stage 1 to stage 2 was possibly induced by sea-level rise, when the Tibetan Tethys Himalaya was located at tropical/subtropical latitudes in suitable climatic and ecological conditions for carbonate sedimentation. The abrupt change from stage 2 to stage 3 is interpreted as a consequence of the early Toarcian oceanic anoxic event, accompanied by obvious carbon-isotope negative excursion and sea-level rise. The failed recovery from the carbonate crisis in the early Bajocian, with continuing deposition on a low-energy carbonate ramp, is ascribed to the tectonic

Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gallivan, Justin

2012-03-21

Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, CA.

Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Gallivan, Justin

2018-05-01

Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, CA.

The fecal bacteria

USGS Publications Warehouse

Sadowsky, Michael J.; Whitman, Richard L.

2011-01-01

The Fecal Bacteria offers a balanced, integrated discussion of fecal bacteria and their presence and ecology in the intestinal tract of mammals, in the environment, and in the food supply. This volume covers their use in examining and assessing water quality in order to offer protection from illnesses related to swimming in or ingesting contaminated water, in addition to discussing their use in engineering considerations of water quality, modeling, monitoring, and regulations. Fecal bacteria are additionally used as indicators of contamination of ready-to-eat foods and fresh produce. The intestinal environment, the microbial community structure of the gut microbiota, and the physiology and genomics of this broad group of microorganisms are explored in the book. With contributions from an internationally recognized group of experts, the book integrates medicine, public health, environmental, and microbiological topics in order to provide a unique, holistic understanding of fecal bacteria. Moreover, it shows how the latest basic science and applied research findings are helping to solve problems and develop effective management strategies. For example, readers will discover how the latest tools and molecular approaches have led to our current understanding of fecal bacteria and enabled us to improve human health and water quality. The Fecal Bacteria is recommended for microbiologists, clinicians, animal scientists, engineers, environmental scientists, food safety experts, water quality managers, and students. It will help them better understand fecal bacteria and use their knowledge to protect human and environmental health. They can also apply many of the techniques and molecular tools discussed in this book to the study of a broad range of microorganisms in a variety of habitats.

A comparative study of methanol as a supplementary carbon source for enhancing denitrification in primary and secondary anoxic zones.

PubMed

Ginige, Maneesha P; Bowyer, Jocelyn C; Foley, Leah; Keller, Jürg; Yuan, Zhiguo

2009-04-01

A comparative study on the use of methanol as a supplementary carbon source to enhance denitrification in primary and secondary anoxic zones is reported. Three lab-scale sequencing batch reactors (SBR) were operated to achieve nitrogen and carbon removal from domestic wastewater. Methanol was added to the primary anoxic period of the first SBR, and to the secondary anoxic period of the second SBR. No methanol was added to the third SBR, which served as a control. The extent of improvement on the denitrification performance was found to be dependent on the reactor configuration. Addition to the secondary anoxic period is more effective when very low effluent nitrate levels are to be achieved and hence requires a relatively large amount of methanol. Adding a small amount of methanol to the secondary anoxic period may cause nitrite accumulation, which does not improve overall nitrogen removal. In the latter case, methanol should be added to the primary anoxic period. The addition of methanol can also improve biological phosphorus removal by creating anaerobic conditions and increasing the availability of organic carbon in wastewater for polyphosphate accumulating organisms. This potentially provides a cost-effective approach to phosphorus removal from wastewater with a low carbon content. New fluorescence in situ hybridisation (FISH) probes targeting methanol-utilising denitrifiers were designed using stable isotope probing. Microbial structure analysis of the sludges using the new and existing FISH probes clearly showed that the addition of methanol stimulated the growth of specific methanol-utilizing denitrifiers, which improved the capability of sludge to use methanol and ethanol for denitrification, but reduced its capability to use wastewater COD for denitrification. Unlike acetate, long-term application of methanol has no negative impact on the settling properties of the sludge.

Carbon isotope fractionation by sulfate-reducing bacteria using different pathways for the oxidation of acetate.

PubMed

Goevert, Dennis; Conrad, Ralf

2008-11-01

Acetate is a key intermediate in the anaerobic degradation of organic matter. In anoxic environments, available acetate is a competitive substrate for sulfate-reducing bacteria (SRB) and methane-producing archaea. Little is known about the fractionation of carbon isotopes by sulfate reducers. Therefore, we determined carbon isotope compositions in cultures of three acetate-utilizing SRB, Desulfobacter postgatei, Desulfobacter hydrogenophilus, and Desulfobacca acetoxidans. We found that these species showed strong differences in their isotope enrichment factors (epsilon) of acetate. During the consumption of acetate and sulfate, acetate was enriched in 13C by 19.3% per hundred in Desulfobacca acetoxidans. By contrast, both D. postgatei and D. hydrogenophilus showed a slight depletion of 13C resulting in epsilon(ac)-values of 1.8 and 1.5% per hundred, respectively. We suggest that the different isotope fractionation is due to the different metabolic pathways for acetate oxidation. The strongly fractionating Desulfobacca acetoxidans uses the acetyl-CoA/carbon monoxide dehydrogenase pathway, which is also used by acetoclastic methanogens that show a similar fractionation of acetate (epsilon(ac) = -21 to -27% per hundred). In contrast, Desulfobacter spp. oxidize acetate to CO2 via the tricarboxylic acid (TCA) cycle and apparently did not discriminate against 13C. Our results suggestthat carbon isotope fractionation in environments with sulfate reduction will strongly depend on the composition of the sulfate-reducing bacterial community oxidizing acetate.

Denitrification by extremely halophilic bacteria

NASA Technical Reports Server (NTRS)

Hochstein, L. I.; Tomlinson, G. A.

1985-01-01

Extremely halophilic bacteria were isolated from widely separated sites by anaerobic enrichment in the presence of nitrate. The anaerobic growth of several of these isolates was accompanied by the production of nitrite, nitrous oxide, and dinitrogen. These results are a direct confirmation of the existence of extremely halophilic denitrifying bacteria, and suggest that such bacteria may be common inhabitants of hypersaline environments.

Ligand-Enhanced Abiotic Iron Oxidation and the Effects of Chemical versus Biological Iron Cycling in Anoxic Environments

PubMed Central

2013-01-01

This study introduces a newly isolated, genetically tractable bacterium (Pseudogulbenkiania sp. strain MAI-1) and explores the extent to which its nitrate-dependent iron-oxidation activity is directly biologically catalyzed. Specifically, we focused on the role of iron chelating ligands in promoting chemical oxidation of Fe(II) by nitrite under anoxic conditions. Strong organic ligands such as nitrilotriacetate and citrate can substantially enhance chemical oxidation of Fe(II) by nitrite at circumneutral pH. We show that strain MAI-1 exhibits unambiguous biological Fe(II) oxidation despite a significant contribution (∼30–35%) from ligand-enhanced chemical oxidation. Our work with the model denitrifying strain Paracoccus denitrificans further shows that ligand-enhanced chemical oxidation of Fe(II) by microbially produced nitrite can be an important general side effect of biological denitrification. Our assessment of reaction rates derived from literature reports of anaerobic Fe(II) oxidation, both chemical and biological, highlights the potential competition and likely co-occurrence of chemical Fe(II) oxidation (mediated by microbial production of nitrite) and truly biological Fe(II) oxidation. PMID:23402562

Vertical distribution and community composition of anammox bacteria in sediments of a eutrophic shallow lake.

PubMed

Qin, H; Han, C; Jin, Z; Wu, L; Deng, H; Zhu, G; Zhong, W

2018-07-01

The aim of this study was to explore the vertical distribution traits of anaerobic ammonium-oxidizing (anammox) bacterial relative abundance and community composition along the oxic/anoxic sediment profiles in a shallow lake. The Illumina Miseq-based sequencing and quantitative polymerase chain reactions were utilized to analyse relative abundance of anammox hydrazine synthase (hzsB) gene in comparison with bacterial 16S rRNA genes, anammox bacterial relative abundance (the number of anammox sequences divided by total number of sequences), community composition and diversity in sediments. The relative abundance of hzsB gene at the low-nitrogen (LN) site in the lake sediments showed that the vertical distribution of anammox bacteria increased to a peak, then decreased with increasing depth. Moreover, the relative abundance of hzsB gene at the high-nitrogen site was significantly lower than that at the LN site. Additionally, the community composition results showed that Candidatus Brocadia sp. was the dominant genus. In addition, the anammox bacterial diversity was also site specific. Redundancy analysis showed that the total N and the NH 4 + -N content might be the most important factors affecting anammox bacterial community composition in the studied sites. The results revealed the specific vertical variance of anammox bacterial distribution and community composition in oxic/anoxic sediments of a eutrophic shallow lake. This is the first study to demonstrate that anammox bacteria displayed the particular distribution in freshwater sediments, which implied a strong response to the anthropogenic eutrophication. © 2018 The Society for Applied Microbiology.

Characteristic Assessment of Diesel-degrading Bacteria Immobilized on Natural Organic Carriers in Marine Environment: the Degradation Activity and Nutrient.

PubMed

Xue, Jianliang; Wu, Yanan; Liu, Zhixiu; Li, Menglu; Sun, Xiyu; Wang, Huajun; Liu, Bing

2017-08-17

Oil spill has led to severe environmental and ecological problems. Due to the harsh environmental conditions, the bioremediation technology is not successfully used to remedy the oil spill in marine environment. In this study, immobilization technology was used to immobilize bacteria on natural organic carriers (i.e., wood chips and maize straw). The higher surface area of in wood chips leads to larger biomass density (0.0242 gVSS/g) than that of maize straw of 0.0097 gVSS/g carrier. Compared with biodegradation efficiency of free bacteria (44.79%), the immobilized bacteria on wood chips and maize straw reached to 73.39% and 52.28%, respectively. The high biological activity of the immobilized bacteria can be also explained by nutrients, such as TN (total nitrogen) and TP (total phosphorus), released from wood chips and maize straw, which was 8.83 mg/g and 5.53 mg/g, 0.0624 mg/g and 0.0099 mg/g, respectively.

Distribution and size fractionation of elemental sulfur in aqueous environments: The Chesapeake Bay and Mid-Atlantic Ridge

NASA Astrophysics Data System (ADS)

Findlay, Alyssa J.; Gartman, Amy; MacDonald, Daniel J.; Hanson, Thomas E.; Shaw, Timothy J.; Luther, George W.

2014-10-01

Elemental sulfur is an important intermediate of sulfide oxidation and may be produced via abiotic and biotic pathways. In this study the concentration and size fractionation of elemental sulfur were measured in two different sulfidic marine environments: the Chesapeake Bay and buoyant hydrothermal vent plumes along the Mid-Atlantic Ridge. Nanoparticulate sulfur (<0.2 μm) was found to comprise up to 90% of the total elemental sulfur in anoxic deep waters of the Chesapeake Bay. These data were compared with previous studies of elemental sulfur, and represent one of the few reports of nanoparticulate elemental sulfur in the environment. Additionally, a strain of phototrophic sulfide oxidizing bacteria isolated from the Chesapeake Bay was shown to produce elemental sulfur as a product of sulfide oxidation. Elemental sulfur concentrations are also presented from buoyant hydrothermal vent plumes located along the Mid-Atlantic Ridge. In the Mid-Atlantic Ridge plume, S0 concentrations up to 33 μM were measured in the first meter of rising plumes at three different vent sites, and nanoparticulate S0 was up to 44% of total elemental sulfur present.

Biogeochemistry of Framvaren, A permanently Anoxic Fjord

NASA Astrophysics Data System (ADS)

Millero, Frank J.

Recently (May 28-30, 1986), a workshop was held in Farsund, Norway, to discuss the biogeochemistry of an anoxic fjord called Framvaren. In the last 7 years a group of marine scientists from Norway, Sweden, Canada, and the United States has been studying this fjord. The workshop was held to discuss the recent findings of this international effort. A new expedition is planned in February 1987 (provided that the ice is thick enough) and in June 1988. Marine chemists, microbiologists, or geologists interested in participating in this study should contact Jens Skei (Norwegian Institute of Water Research, PB Box 333, Blindern, Oslo 3, Norway), who is coordinating the investigations.

Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment.

PubMed

Dobrijevic, Dragana; Abraham, Anne-Laure; Jamet, Alexandre; Maguin, Emmanuelle; van de Guchte, Maarten

2016-01-01

The human GI tract is a complex and still poorly understood environment, inhabited by one of the densest microbial communities on earth. The gut microbiota is shaped by millennia of evolution to co-exist with the host in commensal or symbiotic relationships. Members of the gut microbiota perform specific molecular functions important in the human gut environment. This can be illustrated by the presence of a highly expanded repertoire of proteins involved in carbohydrate metabolism, in phase with the large diversity of polysaccharides originating from the diet or from the host itself that can be encountered in this environment. In order to identify other bacterial functions that are important in the human gut environment, we investigated the distribution of functional groups of proteins in a group of human gut bacteria and their close non-gut relatives. Complementary to earlier global comparisons between different ecosystems, this approach should allow a closer focus on a group of functions directly related to the gut environment while avoiding functions related to taxonomically divergent microbiota composition, which may or may not be relevant for gut homeostasis. We identified several functions that are overrepresented in the human gut bacteria which had not been recognized in a global approach. The observed under-representation of certain other functions may be equally important for gut homeostasis. Together, these analyses provide us with new information about this environment so critical to our health and well-being.

Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment

PubMed Central

Dobrijevic, Dragana; Abraham, Anne-Laure; Jamet, Alexandre; Maguin, Emmanuelle; van de Guchte, Maarten

2016-01-01

The human GI tract is a complex and still poorly understood environment, inhabited by one of the densest microbial communities on earth. The gut microbiota is shaped by millennia of evolution to co-exist with the host in commensal or symbiotic relationships. Members of the gut microbiota perform specific molecular functions important in the human gut environment. This can be illustrated by the presence of a highly expanded repertoire of proteins involved in carbohydrate metabolism, in phase with the large diversity of polysaccharides originating from the diet or from the host itself that can be encountered in this environment. In order to identify other bacterial functions that are important in the human gut environment, we investigated the distribution of functional groups of proteins in a group of human gut bacteria and their close non-gut relatives. Complementary to earlier global comparisons between different ecosystems, this approach should allow a closer focus on a group of functions directly related to the gut environment while avoiding functions related to taxonomically divergent microbiota composition, which may or may not be relevant for gut homeostasis. We identified several functions that are overrepresented in the human gut bacteria which had not been recognized in a global approach. The observed under-representation of certain other functions may be equally important for gut homeostasis. Together, these analyses provide us with new information about this environment so critical to our health and well-being. PMID:27416027

Microbiological and Geochemical Characterization of Fluvially Deposited Sulfidic Mine Tailings

PubMed Central

Wielinga, Bruce; Lucy, Juliette K.; Moore, Johnnie N.; Seastone, October F.; Gannon, James E.

1999-01-01

The fluvial deposition of mine tailings generated from historic mining operations near Butte, Montana, has resulted in substantial surface and shallow groundwater contamination along Silver Bow Creek. Biogeochemical processes in the sediment and underlying hyporheic zone were studied in an attempt to characterize interactions consequential to heavy-metal contamination of shallow groundwater. Sediment cores were extracted and fractionated based on sediment stratification. Subsamples of each fraction were assayed for culturable heterotrophic microbiota, specific microbial guilds involved in metal redox transformations, and both aqueous- and solid-phase geochemistry. Populations of cultivable Fe(III)-reducing bacteria were most prominent in the anoxic, circumneutral pH regions associated with a ferricrete layer or in an oxic zone high in organic carbon and soluble iron. Sulfur- and iron-oxidizing bacteria were distributed in discrete zones throughout the tailings and were often recovered from sections at and below the anoxic groundwater interface. Sulfate-reducing bacteria were also widely distributed in the cores and often occurred in zones overlapping iron and sulfur oxidizers. Sulfate-reducing bacteria were consistently recovered from oxic zones that contained high concentrations of metals in the oxidizable fraction. Altogether, these results suggest a highly varied and complex microbial ecology within a very heterogeneous geochemical environment. Such physical and biological heterogeneity has often been overlooked when remediation strategies for metal contaminated environments are formulated. PMID:10103249

Effects of Bacteria on Artemia franciscana Cultured in Different Gnotobiotic Environments

PubMed Central

Marques, Antonio; Dinh, Thi; Ioakeimidis, Christos; Huys, Geert; Swings, Jean; Verstraete, Willy; Dhont, Jean; Sorgeloos, Patrick; Bossier, Peter

2005-01-01

The use of probiotics is receiving considerable attention as an alternative approach to control microbiota in aquaculture farms, especially in hatching facilities. However, application with consistent results is hampered by insufficient information on their modes of action. To investigate whether dead bacteria (allowing investigation of their nutritional effect) or live bacteria (allowing evaluation of their probiotic effect) have any beneficial effect towards Artemia franciscana and, subsequently, if live bacteria have probiotic effects beyond the effects observed with dead bacteria, a model system was employed using gnotobiotic Artemia as a test organism. Nauplii were cultured in the presence of 10 bacterial strains combined with four different major axenic live feeds (two strains of Saccharomyces cerevisiae and two strains of Dunaliella tertiolecta) differing in their nutritional values. In combination with poor- and medium-quality live feeds, dead bacteria exerted a strong effect on Artemia survival but a rather weak or no effect on individual length and constituted a maximum of only 5.9% of the total ash-free dry weight supplied. These effects were reduced or even disappeared when medium- to good-quality major feed sources were used, possibly due to improvements in the health status of Artemia. Some probiotic bacteria, such as GR 8 (Cytophaga spp.), improved (not always significantly) the performance of nauplii beyond the effect observed with dead bacteria, independently of the feed supplied. The present approach can be an excellent system to study the exact mode of action of bacteria, especially if combined with challenge tests or other types of analysis (e.g., transcriptome and proteonomic analysis). PMID:16085818

Laser-Based Identification of Pathogenic Bacteria

ERIC Educational Resources Information Center

Rehse, Steven J.

2009-01-01

Bacteria are ubiquitous in our world. From our homes, to our work environment, to our own bodies, bacteria are the omnipresent although often unobserved companions to human life. Physicists are typically untroubled professionally by the presence of these bacteria, as their study usually falls safely outside the realm of our typical domain. In the…

Using biogenic sulfur gases as remotely detectable biosignatures on anoxic planets.

PubMed

Domagal-Goldman, Shawn D; Meadows, Victoria S; Claire, Mark W; Kasting, James F

2011-06-01

We used one-dimensional photochemical and radiative transfer models to study the potential of organic sulfur compounds (CS(2), OCS, CH(3)SH, CH(3)SCH(3), and CH(3)S(2)CH(3)) to act as remotely detectable biosignatures in anoxic exoplanetary atmospheres. Concentrations of organic sulfur gases were predicted for various biogenic sulfur fluxes into anoxic atmospheres and were found to increase with decreasing UV fluxes. Dimethyl sulfide (CH(3)SCH(3), or DMS) and dimethyl disulfide (CH(3)S(2)CH(3), or DMDS) concentrations could increase to remotely detectable levels, but only in cases of extremely low UV fluxes, which may occur in the habitable zone of an inactive M dwarf. The most detectable feature of organic sulfur gases is an indirect one that results from an increase in ethane (C(2)H(6)) over that which would be predicted based on the planet's methane (CH(4)) concentration. Thus, a characterization mission could detect these organic sulfur gases-and therefore the life that produces them-if it could sufficiently quantify the ethane and methane in the exoplanet's atmosphere.

Seasonal occurrence of anoxygenic photosynthesis in Tillari and Selaulim reservoirs, Western India

NASA Astrophysics Data System (ADS)

Kurian, S.; Roy, R.; Repeta, D. J.; Gauns, M.; Shenoy, D. M.; Suresh, T.; Sarkar, A.; Narvenkar, G.; Johnson, C. G.; Naqvi, S. W. A.

2012-07-01

Phytoplankton and bacterial pigment compositions were determined by high performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS) in two freshwater reservoirs (Tillari Dam and Selaulim Dam), which are located at the foothills of the Western Ghats in India. These reservoirs experience anoxia in the hypolimnion during summer. Water samples were collected from both reservoirs during anoxic periods while one of them (Tillari Reservoir) was also sampled in winter, when convective mixing results in well-oxygenated conditions throughout the water column. During the period of anoxia (summer), bacteriochlorophyll (BChl) e isomers and isorenieratene, characteristic of brown sulfur bacteria, were dominant in the anoxic (sulfidic) layer of the Tillari Reservoir under low light intensities. The winter observations showed the dominance of small cells of Chlorophyll b-containing green algae and cyanobacteria, with minor presence of fucoxanthin-containing diatoms and peridinin-containing dinoflagellates. Using total BChl e concentration observed in June, the standing stock of brown sulfur bacteria carbon in the anoxic compartment of Tillari Reservoir was estimated to be 2.27 gC m-2, which is much higher than the similar estimate for carbon derived from oxygenic photosynthesis (0.82 gC m-2. The Selaulim Reservoir also displayed similar characteristics with the presence of BChl e isomers and isorenieratene in the anoxic hypolimnion during summer. Although sulfidic conditions prevailed in the water column below the thermocline, the occurrence of photo-autotrophic bacteria was restricted only to mid-depths (maximal concentration of BChl e isomers was detected at 0.2% of the surface incident light). This shows that the vertical distribution of photo-autotrophic sulfur bacteria is primarily controlled by light penetration in the water column where the presence of H2S provides a suitable biogeochemical environment for them to flourish.

Archaeal and bacterial communities respond differently to environmental gradients in anoxic sediments of a California hypersaline lake, the Salton Sea.

PubMed

Swan, Brandon K; Ehrhardt, Christopher J; Reifel, Kristen M; Moreno, Lilliana I; Valentine, David L

2010-02-01

Sulfidic, anoxic sediments of the moderately hypersaline Salton Sea contain gradients in salinity and carbon that potentially structure the sedimentary microbial community. We investigated the abundance, community structure, and diversity of Bacteria and Archaea along these gradients to further distinguish the ecologies of these domains outside their established physiological range. Quantitative PCR was used to enumerate 16S rRNA gene abundances of Bacteria, Archaea, and Crenarchaeota. Community structure and diversity were evaluated by terminal restriction fragment length polymorphism (T-RFLP), quantitative analysis of gene (16S rRNA) frequencies of dominant microorganisms, and cloning and sequencing of 16S rRNA. Archaea were numerically dominant at all depths and exhibited a lesser response to environmental gradients than that of Bacteria. The relative abundance of Crenarchaeota was low (0.4 to 22%) at all depths but increased with decreased carbon content and increased salinity. Salinity structured the bacterial community but exerted no significant control on archaeal community structure, which was weakly correlated with total carbon. Partial sequencing of archaeal 16S rRNA genes retrieved from three sediment depths revealed diverse communities of Euryarchaeota and Crenarchaeota, many of which were affiliated with groups previously described from marine sediments. The abundance of these groups across all depths suggests that many putative marine archaeal groups can tolerate elevated salinity (5.0 to 11.8% [wt/vol]) and persist under the anaerobic conditions present in Salton Sea sediments. The differential response of archaeal and bacterial communities to salinity and carbon patterns is consistent with the hypothesis that adaptations to energy stress and availability distinguish the ecologies of these domains.

Treatment of raw and ozonated oil sands process-affected water under decoupled denitrifying anoxic and nitrifying aerobic conditions: a comparative study.

PubMed

Xue, Jinkai; Zhang, Yanyan; Liu, Yang; Gamal El-Din, Mohamed

2016-11-01

Batch experiments were performed to evaluate biodegradation of raw and ozonated oil sands process-affected water (OSPW) under denitrifying anoxic and nitrifying aerobic conditions for 33 days. The results showed both the anoxic and aerobic conditions are effective in degrading OSPW classical and oxidized naphthenic acids (NAs) with the aerobic conditions demonstrating higher removal efficiency. The reactors under nitrifying aerobic condition reduced the total classical NAs of raw OSPW by 69.1 %, with better efficiency for species of higher hydrophobicity. Compared with conventional aerobic reactor, nitrifying aerobic condition substantially shortened the NA degradation half-life to 16 days. The mild-dose ozonation remarkably accelerated the subsequent aerobic biodegradation of classical NAs within the first 14 days, especially for those with long carbon chains. Moreover, the ozone pretreatment enhanced the biological removal of OSPW classical NAs by leaving a considerably lower final residual concentration of 10.4 mg/L under anoxic conditions, and 5.7 mg/L under aerobic conditions. The combination of ozonation and nitrifying aerobic biodegradation removed total classical NAs by 76.5 % and total oxy-NAs (O3-O6) by 23.6 %. 454 Pyrosequencing revealed that microbial species capable of degrading recalcitrant hydrocarbons were dominant in all reactors. The most abundant genus in the raw and ozonated anoxic reactors was Thauera (~56 % in the raw OSPW anoxic reactor, and ~65 % in the ozonated OSPW anoxic reactor); whereas Rhodanobacter (~40 %) and Pseudomonas (~40 %) dominated the raw and ozonated aerobic reactors, respectively. Therefore, the combination of mild-dose ozone pretreatment and subsequent biological process could be a competent choice for OSPW treatment.

Unexpected photoreactivation of Vibrio harveyi bacteria living in ionization environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alifano, P.; Tala, A.; Tredici, S. M.

2011-05-15

Bacteria undergoing environmental effects is extremely interesting for structural, mechanistic, and evolutionary implications. Luminescent bacteria that have evolved in a specific ambient have developed particular responses and their behavior can give us new suggestions on the task and production of luciferina proteins. To analyze the UV interaction under controlled laboratory conditions, we used photoluminescent bacterial strains belonging to a new species evolutionarily close to Vibrio harveyi sampled from a coastal cave with a high radon content that generates ionizing radiation. The survival of the bacterial strains was analyzed, in the light and in the dark, following a variety of genotoxicmore » treatments including UV radiation exposure. The strains were irradiated by a germicide lamp. The results demonstrated that most of the strains exhibited a low rate of survival after the UV exposure. After irradiation by visible light following the UV exposure, all strains showed a high capability of photoreactivation when grown. This capability was quite unexpected because these bacteria were sampled from a dark ambient without UV radiation. This leads us to hypothesize that the photoreactivation in these bacteria might have been evolved to repair DNA lesions also induced by different radiation sources other than UV (e.g., x-ray) and that the luminescent bacteria might use their own light emission to carry out the photoreactivation. The high capability of photoreactivation of these bacteria was also justified by the results of deconvolution. The deconvolution was applied to the emission spectra and it was able to show evidence of different light peaks. The presence of the visible peak could control the photolysis enzyme.« less

Coexistence of Lactic Acid Bacteria and Potential Spoilage Microbiota in a Dairy Processing Environment

PubMed Central

Stellato, Giuseppina; De Filippis, Francesca; La Storia, Antonietta

2015-01-01

Microbial contamination in food processing plants can play a fundamental role in food quality and safety. In this study, the microbiota in a dairy plant was studied by both 16S rRNA- and 26S rRNA-based culture-independent high-throughput amplicon sequencing. Environmental samples from surfaces and tools were studied along with the different types of cheese produced in the same plant. The microbiota of environmental swabs was very complex, including more than 200 operational taxonomic units with extremely variable relative abundances (0.01 to 99%) depending on the species and sample. A core microbiota shared by 70% of the samples indicated a coexistence of lactic acid bacteria with a remarkable level of Streptococcus thermophilus and possible spoilage-associated bacteria, including Pseudomonas, Acinetobacter, and Psychrobacter, with a relative abundance above 50%. The most abundant yeasts were Kluyveromyces marxianus, Yamadazyma triangularis, Trichosporon faecale, and Debaryomyces hansenii. Beta-diversity analyses showed a clear separation of environmental and cheese samples based on both yeast and bacterial community structure. In addition, predicted metagenomes also indicated differential distribution of metabolic pathways between the two categories of samples. Cooccurrence and coexclusion pattern analyses indicated that the occurrence of potential spoilers was excluded by lactic acid bacteria. In addition, their persistence in the environment can be helpful to counter the development of potential spoilers that may contaminate the cheeses, with possible negative effects on their microbiological quality. PMID:26341209

Diversity and Variability of Geoporphyrins and Chlorins During Cretaceous Oceanic Anoxic Event II.

NASA Astrophysics Data System (ADS)

Junium, C. K.; Mawson, D. H.; Arthur, M. A.; Keely, B. J.

2005-12-01

Geoporphyrins and chlorins are biomarkers that result from the transformation of tetrapyrroles including chlorophylls, bacteriochlorophylls and haems. The transformation reactions are initiated in the water column and sediments during early diagenesis and are dependent on a range of variables including, but not limited to water column redox state, burial conditions, and time. Geoporphyrins and chlorins can retain structural characteristics that allow unambiguous assignment of precursor structures and source organisms making their utility in paleoenvironmental studies extraordinary where such information is preserved. Black shales from Oceanic Anoxic Event II (OAE II, Cenomanian-Turonian Boundary) of ODP Leg 207 present a unique opportunity for investigating the variations in the tetrapyrrole record in very well preserved sediments across a globally significant biogeochemcal event. Identification and structural assignment of tetrapyrroles in this study were achieved by a combination of high-performance-liquid-chromatography (HPLC)/diode-array-detection (DAD) and liquid chromatography-mass spectrometry (LC-MSn) on acetone extracts. Stratigraphic variations in geoporphyrin compounds occur through OAE II. The relative proportions of metallated vs. free-base (metal free) porphyrins vary throughout the sequence, favoring free-base porphyrins during the height of the anoxic event. The greater proportion of free-base porphyrins associated with more extensive reducing conditions is consistent with metal ion limitation during euxinia. For example, vanadyl porphyrins become much less abundant during the peak of the event suggesting that the oceanic inventory of V was sequestered in black shales and unavailable. Preliminary characterization of the tetrapyrroles through OAE II of ODP Leg 207, Demerara Rise, reveals a wide range of geoporphyrins and chlorins. Notably, positive identification of chlorins, the geologically unstable intermediates between highly reactive

Poor outcome prediction by burst suppression ratio in adults with post-anoxic coma without hypothermia.

PubMed

Yang, Qinglin; Su, Yingying; Hussain, Mohammed; Chen, Weibi; Ye, Hong; Gao, Daiquan; Tian, Fei

2014-05-01

Burst suppression ratio (BSR) is a quantitative electroencephalography (qEEG) parameter. The purpose of our study was to compare the accuracy of BSR when compared to other EEG parameters in predicting poor outcomes in adults who sustained post-anoxic coma while not being subjected to therapeutic hypothermia. EEG was registered and recorded at least once within 7 days of post-anoxic coma onset. Electrodes were placed according to the international 10-20 system, using a 16-channel layout. Each EEG expert scored raw EEG using a grading scale adapted from Young and scored amplitude-integrated electroencephalography tracings, in addition to obtaining qEEG parameters defined as BSR with a defined threshold. Glasgow outcome scales of 1 and 2 at 3 months, determined by two blinded neurologists, were defined as poor outcome. Sixty patients with Glasgow coma scale score of 8 or less after anoxic accident were included. The sensitivity (97.1%), specificity (73.3%), positive predictive value (82.5%), and negative prediction value (95.0%) of BSR in predicting poor outcome were higher than other EEG variables. BSR1 and BSR2 were reliable in predicting death (area under the curve > 0.8, P < 0.05), with the respective cutoff points being 39.8% and 61.6%. BSR1 was reliable in predicting poor outcome (area under the curve  =  0.820, P < 0.05) with a cutoff point of 23.9%. BSR1 was also an independent predictor of increased risk of death (odds ratio  =  1.042, 95% confidence intervals: 1.012-1.073, P  =  0.006). BSR may be a better predictor in prognosticating poor outcomes in patients with post-anoxic coma who do not undergo therapeutic hypothermia when compared to other qEEG parameters.

Cardiac pacing for severe childhood neurally mediated syncope with reflex anoxic seizures

PubMed Central

McLeod, K; Wilson, N; Hewitt, J; Norrie, J; Stephenson, J

1999-01-01

OBJECTIVE—To determine whether permanent cardiac pacing could prevent syncope and seizures in children with frequent severe neurally mediated syncope, and if so whether dual chamber pacing was superior to single chamber ventricular pacing.
METHODS—Dual chamber pacemakers were implanted into 12 children (eight male, four female) aged 2-14 years (median 2.8 years) with frequent episodes of reflex anoxic seizures and a recorded prolonged asystole during an attack. The pacemaker was programmed to sensing only (ODO), single chamber ventricular pacing with hysteresis (VVI), and dual chamber pacing with rate drop response (DDD) for four month periods, with each patient allocated to one of the six possible sequences of these modes, according to chronological order of pacemaker implantation. The parent and patient were blinded to the pacemaker mode and asked to record all episodes of syncope or presyncope ("near miss" events). The doctor analysing the results was blinded to the patient and pacemaker mode.
RESULTS—One patient was withdrawn from the study after the pacemaker was removed because of infection. In the remaining children, both dual chamber and single chamber pacing significantly reduced the number of syncopal episodes compared with sensing only (p = 0.0078 for both). VVI was as effective as DDD for preventing syncope, but DDD was superior to VVI in reducing near miss events (p = 0.016).
CONCLUSIONS—Permanent pacing is an effective treatment for children with severe neurally mediated syncope and reflex anoxic seizures. VVI is as effective as DDD in preventing syncope and seizures, but DDD is superior in preventing overall symptoms.


Keywords: syncope; reflex anoxic seizures; pacing; paediatric cardiology PMID:10573501

New glycyl radical enzymes catalysing key metabolic steps in anaerobic bacteria.

PubMed

Selmer, Thorsten; Pierik, Antonio J; Heider, Johann

2005-10-01

During the last decade, an increasing number of new enzymes containing glycyl radicals in their active sites have been identified and biochemically characterised. These include benzylsuccinate synthase (Bss), 4-hydroxyphenylacetate decarboxylase (Hpd) and the coenzyme B12-independent glycerol dehydratase (Gdh). These are involved in metabolic pathways as different as anaerobic toluene metabolism, fermentative production of p-cresol and glycerol fermentation. Some features of these newly discovered enzymes are described and compared with those of the previously known glycyl radical enzymes pyruvate formate-lyase (Pfl) and anaerobic ribonucleotide reductase (Nrd). Among the new enzymes, Bss and Hpd share the presence of small subunits, the function of which in the catalytic mechanisms is still enigmatic, and both enzymes contain metal centres in addition to the glycyl radical prosthetic group. The activating enzymes of the novel systems also deviate from the standard type, containing at least one additional Fe-S cluster. Finally, the available whole-genome sequences of an increasing number of strictly or facultative anaerobic bacteria revealed the presence of many more hitherto unknown glycyl radical enzyme (GRE) systems. Recent studies suggest that the particular types of these enzymes represent the ends of different evolutionary lines, which emerged early in evolution and diversified to yield remarkably versatile biocatalysts for chemical reactions that are otherwise difficult to perform in anoxic environments.

Bacteria Mediate Methylation of Iodine in Marine and Terrestrial Environments

PubMed Central

Amachi, Seigo; Kamagata, Yoichi; Kanagawa, Takahiro; Muramatsu, Yasuyuki

2001-01-01

Methyl iodide (CH3I) plays an important role in the natural iodine cycle and participates in atmospheric ozone destruction. However, the main source of this compound in nature is still unclear. Here we report that a wide variety of bacteria including terrestrial and marine bacteria are capable of methylating the environmental level of iodide (0.1 μM). Of the strains tested, Rhizobium sp. strain MRCD 19 was chosen for further analysis, and it was found that the cell extract catalyzed the methylation of iodide with S-adenosyl-l-methionine as the methyl donor. These results strongly indicate that bacteria contribute to iodine transfer from the terrestrial and marine ecosystems into the atmosphere. PMID:11375186

Analysis of Ecological Distribution and Genomic Content from a Clade of Bacteroidetes Endemic to Sulfidic Environments

NASA Astrophysics Data System (ADS)

Zhou, K.; Sylvan, J. B.; Hallam, S. J.

2017-12-01

The Bacteroidetes are a ubiquitous phylum of bacteria found in a wide variety of habitats. Marine Bacteroidetes are known to utilize complex carbohydrates and have a potentially important role in the global carbon cycle through processing these compounds, which are not digestible by many other microbes. Some members of the phylum are known to perform denitrification and are facultative anaerobes, but Bacteroidetes are not known to participate in sulfur redox cycling. Recently, it was shown that a clade of uncultured Bacteroidetes, including the VC2.1_Bac22 group, appears to be endemic to sulfidic environments, including hydrothermal vent sulfide chimneys, sediments and marine water column oxygen minimum zones (OMZs). This clade, dubbed the Sulfiphilic Bacteroidetes, is not detected in 16S rRNA amplicon studies from non-sulfidic environments. To test the hypothesis that the Sulphiphilic Bacteroidetes are involved in sulfur redox chemistry, we updated our meta-analysis of the clade using 16s rRNA sequences from public databases and employed single-cell genomics to survey their genomic potential using 19 single amplified genomes (SAGs) isolated from the seasonally anoxic Saanich Inlet, a seasonally hypoxic basin in British Columbia. Initial analysis of these SAGs indicates the Sulphiphilic Bacteroidetes may perform sulfur redox reactions using a three gene psrABC operon encoding the polysulfide reductase enzyme complex with a thiosulfate sulfurtransferase (rhodanese), which putatively uses cyanide to convert thiosulfate to sulfite, just upstream. Interestingly, this is the same configuration as discovered recently in some Marine Group A bacteria. Further aspects of the Sulphiphilic Bacteroidetes' genomic potential will be presented in light of their presence in sulfidic environments.

Simultaneous denitrification and denitrifying phosphorus removal in a full-scale anoxic-oxic process without internal recycle treating low strength wastewater.

PubMed

Wang, Qibin; Chen, Qiuwen

2016-01-01

Performance of a full-scale anoxic-oxic activated sludge treatment plant (4.0×10(5) m(3)/day for the first-stage project) was followed during a year. The plant performed well for the removal of carbon, nitrogen and phosphorus in the process of treating domestic wastewater within a temperature range of 10.8°C to 30.5°C. Mass balance calculations indicated that COD utilization mainly occurred in the anoxic phase, accounting for 88.2% of total COD removal. Ammonia nitrogen removal occurred 13.71% in the anoxic zones and 78.77% in the aerobic zones. The contribution of anoxic zones to total nitrogen (TN) removal was 57.41%. Results indicated that nitrogen elimination in the oxic tanks was mainly contributed by simultaneous nitrification and denitrification (SND). The reduction of phosphorus mainly took place in the oxic zones, 61.46% of the total removal. Denitrifying phosphorus removal was achieved biologically by 11.29%. Practical experience proved that adaptability to gradually changing temperature of the microbial populations was important to maintain the plant overall stability. Sudden changes in temperature did not cause paralysis of the system just lower removal efficiency, which could be explained by functional redundancy of microorganisms that may compensate the adverse effects of temperature changes to a certain degree. Anoxic-oxic process without internal recycling has great potential to treat low strength wastewater (i.e., TN<35 mg/L) as well as reducing operation costs. Copyright © 2015. Published by Elsevier B.V.

Rapid quantitative estimation of chlorinated methane utilizing bacteria in drinking water and the effect of nanosilver on biodegradation of the trichloromethane in the environment.

PubMed

Zamani, Isaac; Bouzari, Majid; Emtiazi, Giti; Fanaei, Maryam

2015-03-01

Halomethanes are toxic and carcinogenic chemicals, which are widely used in industry. Also they can be formed during water disinfection by chlorine. Biodegradation by methylotrophs is the most important way to remove these pollutants from the environment. This study aimed to represent a simple and rapid method for quantitative study of halomethanes utilizing bacteria in drinking water and also a method to facilitate the biodegradation of these compounds in the environment compared to cometabolism. Enumeration of chlorinated methane utilizing bacteria in drinking water was carried out by most probable number (MPN) method in two steps. First, the presence and the number of methylotroph bacteria were confirmed on methanol-containing medium. Then, utilization of dichloromethane was determined by measuring the released chloride after the addition of 0.04 mol/L of it to the growth medium. Also, the effect of nanosilver particles on biodegradation of multiple chlorinated methanes was studied by bacterial growth on Bushnell-Haas Broth containing chloroform (trichloromethane) that was treated with 0.2 ppm nanosilver. Most probable number of methylotrophs and chlorinated methane utilizing bacteria in tested drinking water were 10 and 4 MPN Index/L, respectively. Chloroform treatment by nanosilver leads to dechlorination and the production of formaldehyde. The highest growth of bacteria and formic acid production were observed in the tubes containing 1% chloroform treated with nanosilver. By combining the two tests, a rapid approach to estimation of most probable number of chlorinated methane utilizing bacteria is introduced. Treatment by nanosilver particles was resulted in the easier and faster biodegradation of chloroform by bacteria. Thus, degradation of these chlorinated compounds is more efficient compared to cometabolism.

Biogeochemical impacts of aquifer thermal energy storage at 5, 12, 25 and 60°C investigated with anoxic column experiments

NASA Astrophysics Data System (ADS)

Bonte, M.; van Breukelen, B. M.; Van Der Wielen, P. W. J. J.; Stuyfzand, P. J.

2012-04-01

Aquifer thermal energy storage (ATES) uses groundwater to store energy for heating or cooling purposes in the built environment. ATES systems are often located in the same aquifers used for public drinking water supply, leading to urgent questions on its environmental impacts. This contribution presents the results of research on the biogeochemical impacts of ATES in anoxic column experiments at 5, 12, 25, and 60° C. In- and effluents are analyzed for major ions, trace elements, heavy metals, dissolved organic carbon (DOC) and UV extinction. Terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes and analysis of adenosine triphosphate (ATP) were used to detect changes in the microbiological population and activity. Results from the column experiments at 5, 25, and 60° C compared to the reference column at 12° C showed a number of changes in biogeochemical conditions: At 5° C, only changes were observed in alkalinity and calcium concentrations, resulting from calcite dissolution. The 25° C and 60° C column effluents from a sediment containing Fe-(hydr)oxides showed an increase in arsenic concentrations, well above the drinking water limit. This is due to either (reductive) dissolution of, or desorption from, iron(hydro)xides containing arsenic. In addition, at these two temperatures sulfate reduction occurred while this was undetectable at 5 and 12° C within the given timeframe (25 days) and analytical accuracy. The carbon source for sulfate reduction is inferred to be sedimentary organic carbon. Increasing DOC with residence time in the 60° C effluent suggests that at 60° C the terminal sulfate reduction step is rate limiting, while at 25° C the enzymatic hydrolization step in sulfate reducing bacteria is overall rate limiting. Specific ultraviolet absorption (SUVA, the ratio of UV extinction and DOC) however shows a clear decrease in reactivity of the humic acid fraction in DOC. This means that the DOC accumulation at 60° C could

Bacteria and game theory: the rise and fall of cooperation in spatially heterogeneous environments.

PubMed

Lambert, Guillaume; Vyawahare, Saurabh; Austin, Robert H

2014-08-06

One of the predictions of game theory is that cooperative behaviours are vulnerable to exploitation by selfish individuals, but this result seemingly contradicts the survival of cooperation observed in nature. In this review, we will introduce game theoretical concepts that lead to this conclusion and show how the spatial competition dynamics between microorganisms can be used to model the survival and maintenance of cooperation. In particular, we focus on how Escherichia coli bacteria with a growth advantage in stationary phase (GASP) phenotype maintain a proliferative phenotype when faced with overcrowding to gain a fitness advantage over wild-type populations. We review recent experimental approaches studying the growth dynamics of competing GASP and wild-type strains of E. coli inside interconnected microfabricated habitats and use a game theoretical approach to analyse the observed inter-species interactions. We describe how the use of evolutionary game theory and the ideal free distribution accurately models the spatial distribution of cooperative and selfish individuals in spatially heterogeneous environments. Using bacteria as a model system of cooperative and selfish behaviours may lead to a better understanding of the competition dynamics of other organisms-including tumour-host interactions during cancer development and metastasis.

Bioprecipitation of Calcium Carbonate Crystals by Bacteria Isolated from Saline Environments Grown in Culture Media Amended with Seawater and Real Brine

PubMed Central

Silva-Castro, G. A.; Uad, I.; Gonzalez-Martinez, A.; Rivadeneyra, A.; Gonzalez-Lopez, J.; Rivadeneyra, M. A.

2015-01-01

The precipitation of calcium carbonate and calcium sulphate by isolated bacteria from seawater and real brine obtained in a desalination plant growth in culture media containing seawater and brine as mineral sources has been studied. However, only bioprecipitation was detected when the bacteria were grown in media with added organic matter. Biomineralization process started rapidly, crystal formation taking place in the beginning a few days after inoculation of media; roughly 90% of total cultivated bacteria showed. Six major colonies with carbonate precipitation capacity dominated bacterial community structure cultivated in heterotrophic platable bacteria medium. Taxonomic identification of these six strains through partial 16S rRNA gene sequences showed their affiliation with Gram-positive Bacillus and Virgibacillus genera. These strains were able to form calcium carbonate minerals, which precipitated as calcite and aragonite crystals and showed bacterial fingerprints or bacteria calcification. Also, carbonic anhydrase activity was observed in three of these isolated bacteria. The results of this research suggest that microbiota isolated from sea water and brine is capable of precipitation of carbonate biominerals, which can occur in situ with mediation of organic matter concentrations. Moreover, calcium carbonate precipitation ability of this microbiota could be of importance in bioremediation of CO2 and calcium in certain environments. PMID:26273646

Bioprecipitation of Calcium Carbonate Crystals by Bacteria Isolated from Saline Environments Grown in Culture Media Amended with Seawater and Real Brine.

PubMed

Silva-Castro, G A; Uad, I; Gonzalez-Martinez, A; Rivadeneyra, A; Gonzalez-Lopez, J; Rivadeneyra, M A

2015-01-01

The precipitation of calcium carbonate and calcium sulphate by isolated bacteria from seawater and real brine obtained in a desalination plant growth in culture media containing seawater and brine as mineral sources has been studied. However, only bioprecipitation was detected when the bacteria were grown in media with added organic matter. Biomineralization process started rapidly, crystal formation taking place in the beginning a few days after inoculation of media; roughly 90% of total cultivated bacteria showed. Six major colonies with carbonate precipitation capacity dominated bacterial community structure cultivated in heterotrophic platable bacteria medium. Taxonomic identification of these six strains through partial 16S rRNA gene sequences showed their affiliation with Gram-positive Bacillus and Virgibacillus genera. These strains were able to form calcium carbonate minerals, which precipitated as calcite and aragonite crystals and showed bacterial fingerprints or bacteria calcification. Also, carbonic anhydrase activity was observed in three of these isolated bacteria. The results of this research suggest that microbiota isolated from sea water and brine is capable of precipitation of carbonate biominerals, which can occur in situ with mediation of organic matter concentrations. Moreover, calcium carbonate precipitation ability of this microbiota could be of importance in bioremediation of CO2 and calcium in certain environments.

Remediation of TCE-contaminated groundwater using nanocatalyst and bacteria.

PubMed

Kang, Ser Ku; Seo, Hyunhee; Sun, Eunyoung; Kim, Inseon; Roh, Yul

2011-08-01

The objective of this study was to develop and evaluate the remediation of trichloroethene (TCE)-contaminated groundwater using both a nanocatalyst (bio-Zn-magnetite) and bacterium (similar to Clostridium quinii) in anoxic environments. Of the 7 nanocatalysts tested, bio-Zn-magnetite showed the highest TCE dechlorination efficiency, with an average of ca. 90% within 8 days in a batch experiment. The column tests confirmed that the application of bio-Zn-magnetite in combination with the bacterium achieved high degradation efficiency (ca. 90%) of TCE within 5 days compared to the nanocatalyst only, which degraded only 30% of the TCE. These results suggest that the application of a nanocatalyst and the bacterium have potential for the remediation of TCE-contaminated groundwater in subsurface environments.

Anoxic and oxic removal of humic acids with Fe@Fe2O3 core-shell nanowires: a comparative study.

PubMed

Wu, Hao; Ai, Zhihui; Zhang, Lizhi

2014-04-01

In this study we comparatively investigate the removal of humic acids with Fe@Fe2O3 core-shell nanowires under anoxic and oxic conditions. The products of humic acids after reacting with Fe@Fe2O3 core-shell nanowires under anoxic and oxic conditions were carefully examined with three-dimensional excitation emission matrix fluorescence spectroscopy and gas chromatography mass spectrometry. It was found that humic acids were removed by Fe@Fe2O3 core-shell nanowires via adsorption under anoxic condition. Langmuir adsorption isotherm was applicable to describe the adsorption processes. Kinetics of humic acids adsorption onto Fe@Fe2O3 core-shell nanowires was found to follow pseudo-second-order rate equation. By contrast, the oxic removal of humic acids with Fe@Fe2O3 core-shell nanowires involved adsorption and subsequent oxidation of humic acids because Fe@Fe2O3 core-shell nanowires could activate molecular oxygen to produce reactive oxygen species to oxidize humic acids. This subsequent oxidation of humic acids could improve the oxic removal rate to 2.5 times that of anoxic removal, accompanying with about 8.4% of mineralization. This study provides a new method for humic acids removal and also sheds light on the effects of humic acids on the pollutant removal by nano zero-valent iron. Copyright © 2014 Elsevier Ltd. All rights reserved.

Growth of Serratia liquefaciens under 7 mbar, 0°C, and CO2-Enriched Anoxic Atmospheres

PubMed Central

Ulrich, Richard; Berry, Bonnie J.; Nicholson, Wayne L.

2013-01-01

Abstract Twenty-six strains of 22 bacterial species were tested for growth on trypticase soy agar (TSA) or sea-salt agar (SSA) under hypobaric, psychrophilic, and anoxic conditions applied singly or in combination. As each factor was added to multi-parameter assays, the interactive stresses decreased the numbers of strains capable of growth and, in general, reduced the vigor of the strains observed to grow. Only Serratia liquefaciens strain ATCC 27592 exhibited growth at 7 mbar, 0°C, and CO2-enriched anoxic atmospheres. To discriminate between the effects of desiccation and hypobaria, vegetative cells of Bacillus subtilis strain 168 and Escherichia coli strain K12 were grown on TSA surfaces and simultaneously in liquid Luria-Bertani (LB) broth media. Inhibition of growth under hypobaria for 168 and K12 decreased in similar ways for both TSA and LB assays as pressures were reduced from 100 to 25 mbar. Results for 168 and K12 on TSA and LB are interpreted to indicate a direct low-pressure effect on microbial growth with both species and do not support the hypothesis that desiccation alone on TSA was the cause of reduced growth at low pressures. The growth of S. liquefaciens at 7 mbar, 0°C, and CO2-enriched anoxic atmospheres was surprising since S. liquefaciens is ecologically a generalist that occurs in terrestrial plant, fish, animal, and food niches. In contrast, two extremophiles tested in the assays, Deinococcus radiodurans strain R1 and Psychrobacter cryohalolentis strain K5, failed to grow under hypobaric (25 mbar; R1 only), psychrophilic (0°C; R1 only), or anoxic (<0.1% ppO2; both species) conditions. Key Words: Habitable zone—Hypobaria—Extremophiles—Special regions—Planetary protection. Astrobiology 13, 115–131. PMID:23289858

Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria.

PubMed

Sonthiphand, Puntipar; Hall, Michael W; Neufeld, Josh D

2014-01-01

Anaerobic ammonia-oxidizing (anammox) bacteria are able to oxidize ammonia and reduce nitrite to produce N2 gas. After being discovered in a wastewater treatment plant (WWTP), anammox bacteria were subsequently characterized in natural environments, including marine, estuary, freshwater, and terrestrial habitats. Although anammox bacteria play an important role in removing fixed N from both engineered and natural ecosystems, broad scale anammox bacterial distributions have not yet been summarized. The objectives of this study were to explore global distributions and diversity of anammox bacteria and to identify factors that influence their biogeography. Over 6000 anammox 16S rRNA gene sequences from the public database were analyzed in this current study. Data ordinations indicated that salinity was an important factor governing anammox bacterial distributions, with distinct populations inhabiting natural and engineered ecosystems. Gene phylogenies and rarefaction analysis demonstrated that freshwater environments and the marine water column harbored the highest and the lowest diversity of anammox bacteria, respectively. Co-occurrence network analysis indicated that Ca. Scalindua strongly connected with other Ca. Scalindua taxa, whereas Ca. Brocadia co-occurred with taxa from both known and unknown anammox genera. Our survey provides a better understanding of ecological factors affecting anammox bacterial distributions and provides a comprehensive baseline for understanding the relationships among anammox communities in global environments.

Living bacteria in silica gels

NASA Astrophysics Data System (ADS)

Nassif, Nadine; Bouvet, Odile; Noelle Rager, Marie; Roux, Cécile; Coradin, Thibaud; Livage, Jacques

2002-09-01

The encapsulation of enzymes within silica gels has been extensively studied during the past decade for the design of biosensors and bioreactors. Yeast spores and bacteria have also been recently immobilized within silica gels where they retain their enzymatic activity, but the problem of the long-term viability of whole cells in an inorganic matrix has never been fully addressed. It is a real challenge for the development of sol-gel processes. Generic tests have been performed to check the viability of Escherichia coli bacteria in silica gels. Surprisingly, more bacteria remain culturable in the gel than in an aqueous suspension. The metabolic activity of the bacteria towards glycolysis decreases slowly, but half of the bacteria are still viable after one month. When confined within a mineral environment, bacteria do not form colonies. The exchange of chemical signals between isolated bacteria rather than aggregates can then be studied, a point that could be very important for 'quorum sensing'.

Fate of estrogens in a pilot-scale step-feed anoxic/oxic wastewater treatment system controlling by nitrogen and phosphorus removal.

PubMed

Chen, Qingcai; Li, Zebing; Hua, Xiaoyu

2018-05-01

The control measures for estrogens in the aquatic environment are topics of growing concern. It is a meaningful issue to finding optimal process parameters for efficient removal of estrogens with the purpose of efficient total nitrogen (TN) or total phosphorus (TP) removal in sewage treatment plants. The present paper is concerned with the relationships between the estrogen removal and TN or TP removal in a pilot-scale three-stage anoxic/oxic (A/O) system treating real municipal wastewater. The total removal efficiency for estrone (E1) and 17β-estradiol (E2) and their sulfate and glucuronide conjugates were on average 87% in the pilot-scale system. The concentrations of the sulfate and glucuronide conjugates of estrogens (E1 and E2) in the system were much lower than the estrogens, which might be caused by the rapid degradation of conjugates in the pilot-scale system. The average removal efficiencies of E1 and E2 and their sulfate and glucuronide conjugates were significantly lower under high TP removal conditions than those under high TN removal conditions that suggested that the ammonia oxidation promotes estrogen degradation. When the system achieved efficient TN removal, the concentrations of both E1 and E2 were generally lower in the aerobic zones than those in the anoxic zones. Instead, when the system achieved efficient TP removal conditions, the estrogen concentrations were higher in the aerobic zones than in the anoxic zones. However, it was thought that the variation of the concentrations of the estrogen conjugates had weak influence on concentrations of the free estrogens. The increase of the free estrogens in the aerobic zones could be attributed to the release of the estrogens adsorbed on the sludge. The variation of estrogens in a three-stage A/O system can be properly estimated and measured by a binary linear regression model with the variables of TP and TON (NO 2 - -N and NO 3 - -N), which is probably the important information for the improvement

Factors that control the stable carbon isotopic composition of methane produced in an anoxic marine sediment

NASA Technical Reports Server (NTRS)

Alperin, M. J.; Blair, Neal E.; Albert, D. B.; Hoehler, T. M.; Martens, C. S.

1993-01-01

The carbon isotopic composition of methane produced in anoxic marine sediment is controlled by four factors: (1) the pathway of methane formation, (2) the isotopic composition of the methanogenic precursors, (3) the isotope fractionation factors for methane production, and (4) the isotope fractionation associated with methane oxidation. The importance of each factor was evaluated by monitoring stable carbon isotope ratios in methane produced by a sediment microcosm. Methane did not accumulate during the initial 42-day period when sediment contained sulfate, indicating little methane production from 'noncompetitive' substrates. Following sulfate depletion, methane accumulation proceeded in three distinct phases. First, CO2 reduction was the dominant methanogenic pathway and the isotopic composition of the methane produced ranged from -80 to -94 per thousand. The acetate concentration increased during this phase, suggesting that acetoclastic methanogenic bacteria were unable to keep pace with acetate production. Second, acetate fermentation became the dominant methanogenic pathway as bacteria responded to elevated acetate concentrations. The methane produced during this phase was progressively enriched in C-13, reaching a maximum delta(C-13) value of -42 per thousand. Third, the acetate pool experienced a precipitous decline from greater than 5 mM to less than 20 micro-M and methane production was again dominated by CO2 reduction. The delta(C-13) of methane produced during this final phase ranged from -46 to -58 per thousand. Methane oxidation concurrent with methane production was detected throughout the period of methane accumulation, at rates equivalent to 1 to 8 percent of the gross methane production rate. Thus methane oxidation was too slow to have significantly modified the isotopic signature of methane. A comparison of microcosm and field data suggests that similar microbial interactions may control seasonal variability in the isotopic composition of methane

Minerals and Microorganisms in Evaporite Environments

NASA Astrophysics Data System (ADS)

Morris, P. A.; Brigmon, R. L.

2010-12-01

Traditional analysis of evaporite environments have either focused on the geology or the halophilic organisms. It is relatively rare that the two have been combined and even rarer that both disciplines have been incorporated in comparing evaporite sites. The variation in evaporite environments does influence microbial ecology and fossilization processes as each site varies in pH, temperature, presence or absence springs, and spring chemistry. Understanding the evaporite environments is important for planetary scientists as they serve as analogs for evaluating extraterrestrial materials, including the potential for water and ultimately life. For example Mars lander, rover and orbital missions have identified the evaporite signatures of gypsum, carbonates and chlorides, all indicating that water existed at sometime in the planets geological history. Terrestrial evaporite sites all possess halophilic tolerant life. In some instances such as the Dead Sea, Israel, it is restricted to microbial life, but in other sites there are higher life forms. The microbes associated with these evaporite sites can produce biofilms as a method to develop their own microenvironments. Microorganisms can be observed colonizing specific ecological niches or gradients can be created by these environments. These gradients occur due the localized drying and weathering patterns that create different soil chemistry. The microorganisms in turn colonize specific areas more suitable to their specific metabolic needs. For example, under anaerobic conditions with sulfur and methane prevalent methanogenic and/or sulfur reducing microbial species may be observed. However, under similar chemistry environments with the exception of aerobic conditions sulfur oxidizer and/or methanotrophic microorganism may occur. Because of their conspicuous colored pigments purple sulfur bacteria are frequently observed in anoxic zones of lakes, sulfur springs, and stratified evaporite crusts. Some of these bacteria

ARSENIC UPTAKE PROCESSES IN REDUCING ENVIRONMENTS: IMPLICATIONS FOR ACTIVE REMEDIATION AND NATURAL ATTENUATION

EPA Science Inventory

Reductive dissolution of iron oxyhydr(oxides) and release of adsorbed or coprecipitated arsenic is often implicated as a key process that controls the mobility and bioavailability of arsenic in anoxic environments. Yet a complete assessment of arsenic transport and fate requires...

Evidence for the Critical Role of Sucrose Synthase for Anoxic Tolerance of Maize Roots using a Double Mutant

PubMed Central

Ricard, Bérénice; Toai, Tara Van; Chourey, Prem; Saglio, Pierre

1998-01-01

The induction of the sucrose synthase (SuSy) gene (SuSy) by low O2, low temperature, and limiting carbohydrate supply suggested a role in carbohydrate metabolism under stress conditions. The isolation of a maize (Zea mays L.) line mutant for the two known SuSy genes but functionally normal showed that SuSy activity might not be required for aerobic growth and allowed the possibility of investigating its importance during anaerobic stress. As assessed by root elongation after return to air, hypoxic pretreatment improved anoxic tolerance, in correlation with the number of SuSy genes and the level of SuSy expression. Furthermore, root death in double-mutant seedlings during anoxic incubation could be attributed to the impaired utilization of sucrose (Suc). Collectively, these data provide unequivocal evidence that Suc is the principal C source and that SuSy is the main enzyme active in Suc breakdown in roots of maize seedlings deprived of O2. In this situation, SuSy plays a critical role in anoxic tolerance. PMID:9536049

Molybdenum drawdown during Cretaceous Oceanic Anoxic Event 2

NASA Astrophysics Data System (ADS)

Goldberg, Tatiana; Poulton, Simon W.; Wagner, Thomas; Kolonic, Sadat F.; Rehkämper, Mark

2016-04-01

During the Cretaceous greenhouse, episodes of widespread ocean deoxygenation were associated with globally occurring events of black shale deposition. Possibly the most pronounced of these oceanic anoxic events (OAE's) was the Cenomanian-Turonian OAE2 (∼94 Ma). However, although certain redox sensitive trace metals tend to be preferentially sequestered in sediments deposited under anoxic conditions, with Mo drawdown being specifically prone to euxinic settings, these elements are generally somewhat depleted in sediments deposited during OAE2. To understand the driving factors responsible for this depleted trace metal drawdown, we have studied a low latitude section from the proto-North Atlantic Ocean (Tarfaya S57), where existing biomarker and iron-sulphur data point to a dominantly euxinic water column, with periodic transitions to ferruginous (Fe-rich) water column conditions. We utilise a variety of redox proxies (Fe-speciation, redox sensitive trace metals and Mo isotopes), which, in combination, allows us to evaluate the detailed nature of ocean redox conditions and hence controls on trace metal drawdown. The results suggest that seawater δ98Mo values may have ranged between ∼0.6 and 1.1‰ during OAE2, likely connected to changes in the local Mo reservoir as a consequence of low and probably heterogeneous concentrations of Mo in the ocean. The very low Mo/TOC ratios at Tarfaya and elsewhere in the proto-North Atlantic may support a model in which deep-water circulation was partially restricted within and between the North Atlantic and other ocean basins. We propose that the combination of a low and possibly heterogeneous δ98Mo of seawater Mo, together with low Mo/TOC ratios, points to a large decrease in the global oceanic Mo reservoir during OAE2, reflecting a major global scale increase in Mo drawdown under persistent euxinic conditions.

Perils of categorical thinking: "Oxic/anoxic" conceptual model in environmental remediation

USGS Publications Warehouse

Bradley, Paul M.

2012-01-01

Given ambient atmospheric oxygen concentrations of about 21 percent (by volume), the lower limit for reliable quantitation of dissolved oxygen concentrations in groundwater samples is in the range of 0.1–0.5 mg/L. Frameworks for assessing in situ redox condition are often applied using a simple two-category (oxic/anoxic) model of oxygen condition. The "oxic" category defines the environmental range in which dissolved oxygen concentrations are clearly expected to impact contaminant biodegradation, either by supporting aerobic biodegradation of electron-donor contaminants like petroleum hydrocarbons or by inhibiting anaerobic biodegradation of electron-acceptor contaminants like chloroethenes. The tendency to label the second category "anoxic" leads to an invalid assumption that oxygen is insignificant when, in fact, the dissolved oxygen concentration is less than detection but otherwise unknown. Expressing dissolved oxygen concentrations as numbers of molecules per volume, dissolved oxygen concentrations that fall below the 0.1 mg/L field detection limit range from 1 to 1017 molecules/L. In light of recent demonstrations of substantial oxygen-linked biodegradation of chloroethene contaminants at dissolved oxygen concentrations well below the 0.1–0.5 mg/L field detection limit, characterizing "less than detection" oxygen concentrations as "insignificant" is invalid.

Laser-Based Identification of Pathogenic Bacteria

NASA Astrophysics Data System (ADS)

Rehse, Steven J.

2009-03-01

Bacteria are ubiquitous in our world. From our homes, to our work environment, to our own bodies, bacteria are the omnipresent although often unobserved companions to human life. Physicists are typically untroubled professionally by the presence of these bacteria, as their study usually falls safely outside the realm of our typical domain. In the last 10 years, however, several events have occurred that demand the attention of the general populace — including the ranks of physicists among them.

Arsenic redox transformation by Pseudomonas sp. HN-2 isolated from arsenic-contaminated soil in Hunan, China.

PubMed

Zhang, Zhennan; Yin, Naiyi; Cai, Xiaolin; Wang, Zhenzhou; Cui, Yanshan

2016-09-01

A mesophilic, Gram-negative, arsenite[As(III)]-oxidizing and arsenate[As(V)]-reducing bacterial strain, Pseudomonas sp. HN-2, was isolated from an As-contaminated soil. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the strain was closely related to Pseudomonas stutzeri. Under aerobic conditions, this strain oxidized 92.0% (61.4μmol/L) of arsenite to arsenate within 3hr of incubation. Reduction of As(V) to As(III) occurred in anoxic conditions. Pseudomonas sp. HN-2 is among the first soil bacteria shown to be capable of both aerobic As(III) oxidation and anoxic As(V) reduction. The strain, as an efficient As(III) oxidizer and As(V) reducer in Pseudomonas, has the potential to impact arsenic mobility in both anoxic and aerobic environments, and has potential application in As remediation processes. Copyright © 2016. Published by Elsevier B.V.

ENVIRONMENTAL FACTORS INFLUENCING METHANOGENESIS IN A SHALLOW ANOXIC AQUIFER: A FIELD AND LABORATORY STUDY

EPA Science Inventory

The environmental factors influencing methanogenesis in a shallow anoxic aquifer were probed in a combined field and laboratory study. Field data collected over a year revealed that in situ rates of methane production were depressed in winter and elevated in summer. Over the same...

Analysis of mercuric reductase (merA) gene diversity in an anaerobic mercury-contaminated sediment enrichment.

PubMed

Ní Chadhain, Sinéad M; Schaefer, Jeffra K; Crane, Sharron; Zylstra, Gerben J; Barkay, Tamar

2006-10-01

The reduction of ionic mercury to elemental mercury by the mercuric reductase (MerA) enzyme plays an important role in the biogeochemical cycling of mercury in contaminated environments by partitioning mercury to the atmosphere. This activity, common in aerobic environments, has rarely been examined in anoxic sediments where production of highly toxic methylmercury occurs. Novel degenerate PCR primers were developed which span the known diversity of merA genes in Gram-negative bacteria and amplify a 285 bp fragment at the 3' end of merA. These primers were used to create a clone library and to analyse merA diversity in an anaerobic sediment enrichment collected from a mercury-contaminated site in the Meadowlands, New Jersey. A total of 174 sequences were analysed, representing 71 merA phylotypes and four novel MerA clades. This first examination of merA diversity in anoxic environments suggests an untapped resource for novel merA sequences.

Oxygen and sulfur isotope fractionation during sulfide oxidation by anoxygenic phototrophic bacteria

NASA Astrophysics Data System (ADS)

Brabec, Michelle Y.; Lyons, Timothy W.; Mandernack, Kevin W.

2012-04-01

Sulfide-mediated anoxygenic photosynthesis (SMAP) carried out by anaerobic phototrophic bacteria may have played an important role in sulfur cycling, formation of sulfate, and, perhaps, primary production in the Earth’s early oceans. Determination of ε34SSO4-Sulfide- and ε18OSO4-H2O values for bacterial sulfide oxidation will permit more refined interpretation of the δ34S and δ18OSO4 values measured in modern anoxic environments, such as meromictic lakes where sulfide commonly extends into the photic zone, and in the ancient rock record, particularly during periods of the Precambrian when anoxic and sulfidic (euxinic) conditions were believed to be more pervasive than today. Laboratory experiments with anaerobic purple and green sulfur phototrophs, Allochromatium vinosum and Chlorobaculum tepidum, respectively, were conducted to determine the sulfur and oxygen isotope fractionation during the oxidation of sulfide to sulfate. Replicate experiments were conducted at 25 °C for A. vinosum and 45 °C for C. tepidum, and in duplicate at three different starting oxygen isotope values for water to determine sulfate-water oxygen isotope fractionations accurately (ε18OSO4-H2O). ε18OSO4-H2O values of 5.6 ± 0.2‰ and 5.4 ± 0.1‰ were obtained for A. vinosum and C. tepidum, respectively. Temperature had no apparent effect on the ε18OSO4-H2O values. By combining all data from both cultures, an average ε18OSO4-H2O value of 5.6 ± 0.3‰ was obtained for SMAP. This value falls between those previously reported for bacterial oxidation of sphalerite and elemental sulfur (7-9‰) and abiotic and biotic oxidation of pyrite and chalcopyrite (2-4‰). Sulfur isotope fractionation between sulfide and sulfate formed by A.vinosum was negligible (0.1 ± 0.2‰) during all experiments. For C. tepidum an apparent fractionation of -2.3 ± 0.5‰ was observed during the earlier stages of oxidation based on bulk δ34S measurements of sulfate and sulfide and became smaller (-0.7 �

Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria

PubMed Central

Sonthiphand, Puntipar; Hall, Michael W.; Neufeld, Josh D.

2014-01-01

Anaerobic ammonia-oxidizing (anammox) bacteria are able to oxidize ammonia and reduce nitrite to produce N2 gas. After being discovered in a wastewater treatment plant (WWTP), anammox bacteria were subsequently characterized in natural environments, including marine, estuary, freshwater, and terrestrial habitats. Although anammox bacteria play an important role in removing fixed N from both engineered and natural ecosystems, broad scale anammox bacterial distributions have not yet been summarized. The objectives of this study were to explore global distributions and diversity of anammox bacteria and to identify factors that influence their biogeography. Over 6000 anammox 16S rRNA gene sequences from the public database were analyzed in this current study. Data ordinations indicated that salinity was an important factor governing anammox bacterial distributions, with distinct populations inhabiting natural and engineered ecosystems. Gene phylogenies and rarefaction analysis demonstrated that freshwater environments and the marine water column harbored the highest and the lowest diversity of anammox bacteria, respectively. Co-occurrence network analysis indicated that Ca. Scalindua strongly connected with other Ca. Scalindua taxa, whereas Ca. Brocadia co-occurred with taxa from both known and unknown anammox genera. Our survey provides a better understanding of ecological factors affecting anammox bacterial distributions and provides a comprehensive baseline for understanding the relationships among anammox communities in global environments. PMID:25147546

Anaerobic methane oxidation coupled to denitrification is the dominant methane sink in a deep lake

PubMed Central

Deutzmann, Joerg S.; Stief, Peter; Brandes, Josephin; Schink, Bernhard

2014-01-01

Anaerobic methane oxidation coupled to denitrification, also known as “nitrate/nitrite-dependent anaerobic methane oxidation” (n-damo), was discovered in 2006. Since then, only a few studies have identified this process and the associated microorganisms in natural environments. In aquatic sediments, the close proximity of oxygen- and nitrate-consumption zones can mask n-damo as aerobic methane oxidation. We therefore investigated the vertical distribution and the abundance of denitrifying methanotrophs related to Candidatus Methylomirabilis oxyfera with cultivation-independent molecular techniques in the sediments of Lake Constance. Additionally, the vertical distribution of methane oxidation and nitrate consumption zones was inferred from high-resolution microsensor profiles in undisturbed sediment cores. M. oxyfera-like bacteria were virtually absent at shallow-water sites (littoral sediment) and were very abundant at deep-water sites (profundal sediment). In profundal sediment, the vertical distribution of M. oxyfera-like bacteria showed a distinct peak in anoxic layers that coincided with the zone of methane oxidation and nitrate consumption, a strong indication for n-damo carried out by M. oxyfera-like bacteria. Both potential n-damo rates calculated from cell densities (660–4,890 µmol CH4⋅m−2⋅d−1) and actual rates calculated from microsensor profiles (31–437 µmol CH4⋅m−2⋅d−1) were sufficiently high to prevent methane release from profundal sediment solely by this process. Additionally, when nitrate was added to sediment cores exposed to anoxic conditions, the n-damo zone reestablished well below the sediment surface, completely preventing methane release from the sediment. We conclude that the previously overlooked n-damo process can be the major methane sink in stable freshwater environments if nitrate is available in anoxic zones. PMID:25472842

Anaerobic methane oxidation coupled to denitrification is the dominant methane sink in a deep lake.

PubMed

Deutzmann, Joerg S; Stief, Peter; Brandes, Josephin; Schink, Bernhard

2014-12-23

Anaerobic methane oxidation coupled to denitrification, also known as "nitrate/nitrite-dependent anaerobic methane oxidation" (n-damo), was discovered in 2006. Since then, only a few studies have identified this process and the associated microorganisms in natural environments. In aquatic sediments, the close proximity of oxygen- and nitrate-consumption zones can mask n-damo as aerobic methane oxidation. We therefore investigated the vertical distribution and the abundance of denitrifying methanotrophs related to Candidatus Methylomirabilis oxyfera with cultivation-independent molecular techniques in the sediments of Lake Constance. Additionally, the vertical distribution of methane oxidation and nitrate consumption zones was inferred from high-resolution microsensor profiles in undisturbed sediment cores. M. oxyfera-like bacteria were virtually absent at shallow-water sites (littoral sediment) and were very abundant at deep-water sites (profundal sediment). In profundal sediment, the vertical distribution of M. oxyfera-like bacteria showed a distinct peak in anoxic layers that coincided with the zone of methane oxidation and nitrate consumption, a strong indication for n-damo carried out by M. oxyfera-like bacteria. Both potential n-damo rates calculated from cell densities (660-4,890 µmol CH4⋅m(-2)⋅d(-1)) and actual rates calculated from microsensor profiles (31-437 µmol CH4⋅m(-2)⋅d(-1)) were sufficiently high to prevent methane release from profundal sediment solely by this process. Additionally, when nitrate was added to sediment cores exposed to anoxic conditions, the n-damo zone reestablished well below the sediment surface, completely preventing methane release from the sediment. We conclude that the previously overlooked n-damo process can be the major methane sink in stable freshwater environments if nitrate is available in anoxic zones.

The Role of Cell Volume in the Dynamics of Seizure, Spreading Depression, and Anoxic Depolarization

PubMed Central

Ullah, Ghanim; Wei, Yina; Dahlem, Markus A; Wechselberger, Martin; Schiff, Steven J

2015-01-01

Cell volume changes are ubiquitous in normal and pathological activity of the brain. Nevertheless, we know little of how cell volume affects neuronal dynamics. We here performed the first detailed study of the effects of cell volume on neuronal dynamics. By incorporating cell swelling together with dynamic ion concentrations and oxygen supply into Hodgkin-Huxley type spiking dynamics, we demonstrate the spontaneous transition between epileptic seizure and spreading depression states as the cell swells and contracts in response to changes in osmotic pressure. Our use of volume as an order parameter further revealed a dynamical definition for the experimentally described physiological ceiling that separates seizure from spreading depression, as well as predicted a second ceiling that demarcates spreading depression from anoxic depolarization. Our model highlights the neuroprotective role of glial K buffering against seizures and spreading depression, and provides novel insights into anoxic depolarization and the relevant cell swelling during ischemia. We argue that the dynamics of seizures, spreading depression, and anoxic depolarization lie along a continuum of the repertoire of the neuron membrane that can be understood only when the dynamic ion concentrations, oxygen homeostasis,and cell swelling in response to osmotic pressure are taken into consideration. Our results demonstrate the feasibility of a unified framework for a wide range of neuronal behaviors that may be of substantial importance in the understanding of and potentially developing universal intervention strategies for these pathological states. PMID:26273829

Analysis on the Upwelling of the Anoxic Water Mass in Inner Tokyo Bay

NASA Astrophysics Data System (ADS)

Kitahara, Kouichi; Wada, Akira; Kawanaga, Mitsuhito; Fukuoka, Ippei; Takano, Tairyu

In the period of strong density stratification from early summer through early fall, the supply of oxygen from the sea surface to the deeper water is cut off. At the same time, organic matter decomposes near the ocean bottom, so that the anoxic water mass forms. In inner Tokyo Bay, when a northeasterly wind(directed from the inner bay toward the mouth of the bay)blows, the anoxic water mass upwells(an “Aoshio” occurs). In some cases fishes and shellfish die along the coast. Based on the report of results of continuous observations of water temperature, salinity and dissolved oxygen content presented by Fukuoka et al, 2005, here we have used an improved fluid flow model to carry out 3-dimensional calculations of the water level, water temperature, salinity and flow distributions. The computational results have reproduced the observational results well. The calculations showed that upwelling of the anoxic water mass that forms during the stratified period is not only affected by the continuously blowing northeasterly wind, but also by a continuous southwesterly wind that blew several days previously. Surface water blown against the coast by this continuous southwesterly wind is pushed downward; the calculations reproduced the process by which the rising force of this previously downwelled surface water also affects the phenomenon of anoxia. Furthermore, we presented the results of time dependent analysis of quantities relevant to water quality, including dissolved oxygen, which is closely related to the Aoshio, using the flow and diffusion model and a primary ecological model during the stratified ocean period, the sinking period and the upwelling period. We have compared the computed results to the results of continuous observations of dissolved oxygen during occurrence of an Aoshio in 1992 at observation point D-2, and confirmed that this model is an appropriate one to describe this phenomenon.

Cross-regulation by CrcZ RNA controls anoxic biofilm formation in Pseudomonas aeruginosa

NASA Astrophysics Data System (ADS)

Pusic, Petra; Tata, Muralidhar; Wolfinger, Michael T.; Sonnleitner, Elisabeth; Häussler, Susanne; Bläsi, Udo

2016-12-01

Pseudomonas aeruginosa (PA) can thrive in anaerobic biofilms in the lungs of cystic fibrosis (CF) patients. Here, we show that CrcZ is the most abundant PA14 RNA bound to the global regulator Hfq in anoxic biofilms grown in cystic fibrosis sputum medium. Hfq was crucial for anoxic biofilm formation. This observation complied with an RNAseq based transcriptome analysis and follow up studies that implicated Hfq in regulation of a central step preceding denitrification. CrcZ is known to act as a decoy that sequesters Hfq during relief of carbon catabolite repression, which in turn alleviates Hfq-mediated translational repression of catabolic genes. We therefore inferred that CrcZ indirectly impacts on biofilm formation by competing for Hfq. This hypothesis was supported by the findings that over-production of CrcZ mirrored the biofilm phenotype of the hfq deletion mutant, and that deletion of the crcZ gene augmented biofilm formation. To our knowledge, this is the first example where competition for Hfq by CrcZ cross-regulates an Hfq-dependent physiological process unrelated to carbon metabolism.

Lipopolysaccharides in diazotrophic bacteria.

PubMed

Serrato, Rodrigo V

2014-01-01

Biological nitrogen fixation (BNF) is a process in which the atmospheric nitrogen (N2) is transformed into ammonia (NH3) by a select group of nitrogen-fixing organisms, or diazotrophic bacteria. In order to furnish the biologically useful nitrogen to plants, these bacteria must be in constant molecular communication with their host plants. Some of these molecular plant-microbe interactions are very specific, resulting in a symbiotic relationship between the diazotroph and the host. Others are found between associative diazotrophs and plants, resulting in plant infection and colonization of internal tissues. Independent of the type of ecological interaction, glycans, and glycoconjugates produced by these bacteria play an important role in the molecular communication prior and during colonization. Even though exopolysaccharides (EPS) and lipochitooligosaccharides (LCO) produced by diazotrophic bacteria and released onto the environment have their importance in the microbe-plant interaction, it is the lipopolysaccharides (LPS), anchored on the external membrane of these bacteria, that mediates the direct contact of the diazotroph with the host cells. These molecules are extremely variable among the several species of nitrogen fixing-bacteria, and there are evidences of the mechanisms of infection being closely related to their structure.

Lipopolysaccharides in diazotrophic bacteria

PubMed Central

Serrato, Rodrigo V.

2014-01-01

Biological nitrogen fixation (BNF) is a process in which the atmospheric nitrogen (N2) is transformed into ammonia (NH3) by a select group of nitrogen-fixing organisms, or diazotrophic bacteria. In order to furnish the biologically useful nitrogen to plants, these bacteria must be in constant molecular communication with their host plants. Some of these molecular plant-microbe interactions are very specific, resulting in a symbiotic relationship between the diazotroph and the host. Others are found between associative diazotrophs and plants, resulting in plant infection and colonization of internal tissues. Independent of the type of ecological interaction, glycans, and glycoconjugates produced by these bacteria play an important role in the molecular communication prior and during colonization. Even though exopolysaccharides (EPS) and lipochitooligosaccharides (LCO) produced by diazotrophic bacteria and released onto the environment have their importance in the microbe-plant interaction, it is the lipopolysaccharides (LPS), anchored on the external membrane of these bacteria, that mediates the direct contact of the diazotroph with the host cells. These molecules are extremely variable among the several species of nitrogen fixing-bacteria, and there are evidences of the mechanisms of infection being closely related to their structure. PMID:25232535

Bacterial community analysis of anoxic/aeration (A/O) system in a combined process for gibberellin wastewater treatment

PubMed Central

Ouyang, Erming; Lu, Yao; Ouyang, Jiating; Wang, Lele; Wang, Xiaohui

2017-01-01

Gibberellin wastewater cannot be directly discharged without treatment due to its high concentrations of sulfate and organic compounds and strong acidity. Therefore, multi-stage anaerobic bioreactor + micro-aerobic+ anoxic/aeration (A/O) + biological contact oxidation combined processes are used to treat gibberellin wastewater. However, knowledge of the treatment effects of the A/O process and bacterial community structure in the aeration tank reactors of such systems is sparse. Therefore, this study was conducted to investigate the treatment effects and operation of the A/O process on gibberellin wastewater, as well as changes in the bacterial community structure of activated sludge in the aeration tank during treatment. Moreover, removal was examined based on evaluation of effluent after A/O treatment. Although influent chemical oxygen demand (COD), NH3-N and total phosphorus (TP) fluctuated, effluent COD, NH3-N and TP remained stable. Moreover, average COD, NH3-N and TP removal efficiency were 68.41%, 93.67% and 45.82%, respectively, during the A/O process. At the phylum level, Proteobacteria was the dominant phylum in all samples, followed by Chloroflexi, Bacteroidetes and Actinobacteria. Proteobacteria played an important role in the removal of organic matter. Chloroflexi was found to be responsible for the degradation of carbohydrates and Bacteroidetes also had been found to be responsible for the degradation of complex organic matters. Actinobacteria are able to degrade a variety of environmental chemicals. Additionally, Anaerolineaceae_uncultured was the major genus in samples collected on May 25, 2015, while Novosphingobium and Nitrospira were dominant in most samples. Nitrosomonas are regarded as the dominant ammonia-oxidizing bacteria, while Nitrospira are the main nitrite-oxidizing bacteria. Bacterial community structure varied considerably with time, and a partial Mantel test showed a highly significant positive correlation between bacterial community

Influence of aerobic and anoxic microenvironments on polyhydroxyalkanoates (PHA) production from food waste and acidogenic effluents using aerobic consortia.

PubMed

Reddy, M Venkateswar; Mohan, S Venkata

2012-01-01

The functional role of aerobic and anoxic microenvironments on polyhydroxyalkanoates (PHA) production using food waste (UFW) and effluents from acidogenic biohydrogen production process (FFW) were studied employing aerobic mixed culture as biocatalyst. Anoxic microenvironment documented higher PHA production, while aerobic microenvironment showed higher substrate degradation. FFW showed higher PHA accumulation (39.6%) than UFW (35.6%) due to ready availability of precursors (fatty acids). Higher fraction of poly-3-hydroxy butyrate (PHB) was observed compared to poly-3-hydroxy valerate (PHV) in the accumulated PHA in the form of co-polymer [P3(HB-co-HV)]. Dehydrogenase, phosphatase and protease enzymatic activities were monitored during process operation. Integration with fermentative biohydrogen production yielded additional substrate degradation under both aerobic (78%) and anoxic (72%) microenvironments apart from PHA production. Microbial community analysis documented the presence of aerobic and facultative organisms capable of producing PHA. Integration strategy showed feasibility of producing hydrogen along with PHA by consuming fatty acids generated during acidogenic process in association with increased treatment efficiency. Copyright © 2011 Elsevier Ltd. All rights reserved.

Evaluation of mercury biogeochemical cycling at the sediment-water interface in anthropogenically modified lagoon environments.

PubMed

Petranich, Elisa; Covelli, Stefano; Acquavita, Alessandro; Faganeli, Jadran; Horvat, Milena; Contin, Marco

2018-06-01

The Marano and Grado Lagoon is well known for being contaminated by mercury (Hg) from the Idrija mine (Slovenia) and the decommissioned chlor-alkali plant of Torviscosa (Italy). Experimental activities were conducted in a local fish farm to understand Hg cycling at the sediment-water interface. Both diffusive and benthic fluxes were estimated in terms of chemical and physical features. Mercury concentration in sediments (up to 6.81μg/g) showed a slight variability with depth, whereas the highest methylmercury (MeHg) values (up to 10ng/g) were detected in the first centimetres. MeHg seems to be produced and stored in the 2-3cm below the sediment-water interface, where sulphate reducing bacteria activity occurs and hypoxic-anoxic conditions become persistent for days. DMeHg in porewaters varied seasonally (from 0.1 and 17% of dissolved Hg (DHg)) with the highest concentrations in summer. DHg diffusive effluxes higher (up to 444ng/m 2 /day) than those reported in the open lagoon (~95ng/m 2 /day), whereas DMeHg showed influxes in the fish farm (up to -156ng/m 2 /day). The diurnal DHg and DMeHg benthic fluxes were found to be higher than the highest summer values previously reported for the natural lagoon environment. Bottom sediments, especially in anoxic conditions, seem to be a significant source of MeHg in the water column where it eventually accumulates. However, net fluxes considering the daily trend of DHg and DMeHg, indicated possible DMeHg degradation processes. Enhancing water dynamics in the fish farm could mitigate environmental conditions suitable for Hg methylation. Copyright © 2017. Published by Elsevier B.V.

Biogeochemical Cycle of Methanol in Anoxic Deep-Sea Sediments

PubMed Central

Yanagawa, Katsunori; Tani, Atsushi; Yamamoto, Naoya; Hachikubo, Akihiro; Kano, Akihiro; Matsumoto, Ryo; Suzuki, Yohey

2016-01-01

The biological flux and lifetime of methanol in anoxic marine sediments are largely unknown. We herein reported, for the first time, quantitative methanol removal rates in subsurface sediments. Anaerobic incubation experiments with radiotracers showed high rates of microbial methanol consumption. Notably, methanol oxidation to CO2 surpassed methanol assimilation and methanogenesis from CO2/H2 and methanol. Nevertheless, a significant decrease in methanol was not observed after the incubation, and this was attributed to the microbial production of methanol in parallel with its consumption. These results suggest that microbial reactions play an important role in the sources and sinks of methanol in subseafloor sediments. PMID:27301420

Oasis desert farming selects environment-specific date palm root endophytic communities and cultivable bacteria that promote resistance to drought.

PubMed

Cherif, Hanene; Marasco, Ramona; Rolli, Eleonora; Ferjani, Raoudha; Fusi, Marco; Soussi, Asma; Mapelli, Francesca; Blilou, Ikram; Borin, Sara; Boudabous, Abdellatif; Cherif, Ameur; Daffonchio, Daniele; Ouzari, Hadda

2015-08-01

Oases are desert-farming agro-ecosystems, where date palm (Phoenix dactylifera L.) plays a keystone role in offsetting the effects of drought and maintaining a suitable microclimate for agriculture. At present, abundance, diversity and plant growth promotion (PGP) of date palm root-associated bacteria remain unknown. Considering the environmental pressure determined by the water scarcity in the desert environments, we hypothesized that bacteria associated with date palm roots improve plant resistance to drought. Here, the ecology of date palm root endophytes from oases in the Tunisian Sahara was studied with emphasis on their capacity to promote growth under drought. Endophytic communities segregated along a north-south gradient in correlation with geo-climatic parameters. Screening of 120 endophytes indicated that date palm roots select for bacteria with multiple PGP traits. Bacteria rapidly cross-colonized the root tissues of different species of plants, including the original Tunisian date palm cultivar, Saudi Arabian cultivars and Arabidopsis. Selected endophytes significantly increased the biomass of date palms exposed to repeated drought stress periods during a 9-month greenhouse experiment. Overall, results indicate that date palm roots shape endophytic communities that are capable to promote plant growth under drought conditions, thereby contributing an essential ecological service to the entire oasis ecosystem. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Social behavior of bacteria: from physics to complex organization

NASA Astrophysics Data System (ADS)

Ben-Jacob, E.

2008-10-01

I describe how bacteria develop complex colonial patterns by utilizing intricate communication capabilities, such as quorum sensing, chemotactic signaling and exchange of genetic information (plasmids) Bacteria do not store genetically all the information required for generating the patterns for all possible environments. Instead, additional information is cooperatively generated as required for the colonial organization to proceed. Each bacterium is, by itself, a biotic autonomous system with its own internal cellular informatics capabilities (storage, processing and assessments of information). These afford the cell certain plasticity to select its response to biochemical messages it receives, including self-alteration and broadcasting messages to initiate alterations in other bacteria. Hence, new features can collectively emerge during self-organization from the intra-cellular level to the whole colony. Collectively bacteria store information, perform decision make decisions (e.g. to sporulate) and even learn from past experience (e.g. exposure to antibiotics)-features we begin to associate with bacterial social behavior and even rudimentary intelligence. I also take Schrdinger’s’ “feeding on negative entropy” criteria further and propose that, in addition organisms have to extract latent information embedded in the environment. By latent information we refer to the non-arbitrary spatio-temporal patterns of regularities and variations that characterize the environmental dynamics. In other words, bacteria must be able to sense the environment and perform internal information processing for thriving on latent information embedded in the complexity of their environment. I then propose that by acting together, bacteria can perform this most elementary cognitive function more efficiently as can be illustrated by their cooperative behavior.

Sewage treatment effluents in Delhi: A key contributor of β-lactam resistant bacteria and genes to the environment.

PubMed

Lamba, Manisha; Ahammad, Shaikh Ziauddin

2017-12-01

Rapid emergence of antibiotic resistance (AR) in developing countries is posing a greater health risk and increasing the global disease burden. Lack of access to safe drinking water, poor sanitation and inadequate sewage treatment facilities in these countries are fueling the problem associated with emergence of AR. Rapid proliferation of AR mediated by treated and untreated discharges from sewage treatment plants (STPs) is a prime public health concern. This study aims to understand the occurrence, fate, and routes of proliferation of carbapenem (KPC) and extended spectrum β-lactam (ESBL) resistant bacteria, and selected resistant genes in the samples collected from different unit operations in 12 STPs in New Delhi over two seasons. Strong correlation observed between faecal coliform levels and KPC (R = 0.95, p = 0.005, n = 60) and ESBL (R = 0.94, p = 0.004, n = 60) resistant bacteria levels indicates possible association of resistant bacteria with faecal matter. Different unit operations in STPs proved inefficient in treating resistant bacteria and genes present in the wastewater. However, inclusion of tertiary treatment (chlorination) unit and anaerobic digester in the present STPs resulted in better removal of AR. Significant correlations between antibiotic resistant genes (ARGs) and integron levels indicates a potential for higher rate of AR proliferation in the environment. Microbial culturing indicated the presence of clinically significant drug-resistant pathogens such as Escherichia coli, Pseudomonas putida, Pseudomonas aeruginosa, Enterobacter cloacae, Klebsiella pneumoniae, Klebsiella oxytoca, Acinetobacter baumannii, Shigella dysentery and Aeromonas caviae in the STP effluents. The emergence and spread of resistant bacteria through STP effluents poses exposure risk for the residents of the city. Copyright © 2017 Elsevier Ltd. All rights reserved.

Volatilization of mercury compounds by methylmercury-volatilizing bacteria in Minamata Bay sediment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakamura, K.; Sakata, T.; Nakahara, H.

1988-11-01

Minamata Bay has been heavily polluted by high mercury concentrations which gave rise for a long time to methylmercury poisoning, Minamata disease (Kutsuna 1968; Irukayama 1977). The mercury still exists in the sediments of the Bay. The population of mercury-resistant bacteria in the sediments of Minamata Bay is larger than that in the sediments of other marine environments. The mercury-resistant bacteria isolated from a marine environment have been found to transform organic and inorganic mercury compounds into mercury vapor. The mercury-resistance confirmed in various bacterial genera has been shown to be plasmid-mediated volatilization. However, there has been little definitive informationmore » on the volatilization of organic mercury by the bacteria living in the mercury-polluted environment. It is important to know what bacterial transformations of mercury have been taking place and how the mercury-resistant bacteria may be playing a role in the mercury cycle in the marine environment of Minamata Bay. The object of the present study is to clarify the characteristics of the methylmercury-volatilizing bacteria in the sediments of Minamata Bay and of the volatilization of various mercury compounds by these bacteria.« less

Vertical distribution of Fe and Fe(III)-reducing bacteria in the sediments of Lake Donghu, China.

PubMed

Tian, Cuicui; Wang, Chunbo; Tian, Yingying; Wu, Xingqiang; Xiao, Bangding

2015-08-01

In lake sediments, iron (Fe) is the most versatile element, and the redox cycling of Fe has a wide influence on the biogeochemical cycling of organic and inorganic substances. The aim of the present study was to analyze the vertical distribution of Fe and Fe(III)-reducing bacteria (FeRB) in the surface sediment (30 cm) of Lake Donghu, China. At the 3 sites we surveyed, FeRB and Fe(II)-oxidizing bacteria (FeOB) coexisted in anoxic sediments. Geobacter-related FeRB accounted for 5%-31% of the total Bacteria, while Gallionella-related FeOB accounted for only 0.1%-1.3%. A significant correlation between the relative abundance of poorly crystalline Fe and Geobacter spp. suggested that poorly crystalline Fe favored microbial Fe(III) reduction. Poorly crystalline Fe and Geobacter spp. were significantly associated with solid-phase Fe(II) and total inorganic phosphorus levels. Pore water Fe(II) concentrations negatively correlated with NO3(-) at all sites. We concluded that Geobacter spp. were abundant in the sediments of Lake Donghu, and the redox of Fe might participate in the cycling of nitrogen and phosphorus in sediments. These observations provided insight into the roles of microbial Fe cycling in lake sediments.

Integration of organohalide-respiring bacteria and nanoscale zero-valent iron (Bio-nZVI-RD): A perfect marriage for the remediation of organohalide pollutants?

PubMed

Wang, Shanquan; Chen, Siyuan; Wang, Yu; Low, Adrian; Lu, Qihong; Qiu, Rongliang

2016-12-01

Due to massive production and improper handling, organohalide compounds are widely distributed in subsurface environments, primarily in anoxic groundwater, soil and sediment. Compared to traditional pump-and-treat or dredging-and-disposal treatments, in situ remediation employing abiotic or biotic reductive dehalogenation represents a sustainable and economic solution for the removal of organohalide pollutants. Both nanoscale zero-valent iron (nZVI) and organohalide-respiring bacteria remove halogens through reductive dehalogenation and have been extensively studied and successfully applied for the in situ remediation of chloroethenes and other organohalide pollutants. nZVI and microbial reductive dehalogenation (Bio-RD) complement each other to boost reductive dehalogenation efficiency, suggesting that the integration of nZVI with Bio-RD (Bio-nZVI-RD) may constitute an even more promising strategy for the in situ remediation of organohalide pollutants. In this review, we first provide an overview of the current literature pertaining to nZVI- and organohalide-respiring bacteria-mediated reductive dehalogenation of organohalide pollutants and compare the pros and cons of individual treatment methods. We then highlight recent studies investigating the implementation of Bio-nZVI-RD to achieve rapid and complete dehalogenation and discuss the halogen removal mechanism of Bio-nZVI-RD and its prospects for future remediation applications. In summary, the use of Bio-nZVI-RD facilitates opportunities for the effective in situ remediation of a wide range of organohalide pollutants. Copyright © 2016 Elsevier Inc. All rights reserved.

Extremely Halophilic Bacteria in Crystallizer Ponds from Solar Salterns

PubMed Central

Antón, Josefa; Rosselló-Mora, Ramón; Rodríguez-Valera, Francisco; Amann, Rudolf

2000-01-01

It is generally assumed that hypersaline environments with sodium chloride concentrations close to saturation are dominated by halophilic members of the domain Archaea, while Bacteria are not considered to be relevant in this kind of environment. Here, we report the high abundance and growth of a new group of hitherto-uncultured Bacteria in crystallizer ponds (salinity, from 30 to 37%) from multipond solar salterns. In the present study, these Bacteria constituted from 5 to 25% of the total prokaryotic community and were affiliated with the Cytophaga-Flavobacterium-Bacteroides phylum. Growth was demonstrated in saturated NaCl. A provisional classification of this new bacterial group as “Candidatus Salinibacter gen. nov.” is proposed. The perception that Archaea are the only ecologically relevant prokaryotes in hypersaline aquatic environments should be revised. PMID:10877805

Anaerobic degradation of cyclohexane by sulfate-reducing bacteria from hydrocarbon-contaminated marine sediments.

PubMed

Jaekel, Ulrike; Zedelius, Johannes; Wilkes, Heinz; Musat, Florin

2015-01-01

The fate of cyclohexane, often used as a model compound for the biodegradation of cyclic alkanes due to its abundance in crude oils, in anoxic marine sediments has been poorly investigated. In the present study, we obtained an enrichment culture of cyclohexane-degrading sulfate-reducing bacteria from hydrocarbon-contaminated intertidal marine sediments. Microscopic analyses showed an apparent dominance by oval cells of 1.5 × 0.8 μm. Analysis of a 16S rRNA gene library, followed by whole-cell hybridization with group- and sequence-specific oligonucleotide probes showed that these cells belonged to a single phylotype, and were accounting for more than 80% of the total cell number. The dominant phylotype, affiliated with the Desulfosarcina-Desulfococcus cluster of the Deltaproteobacteria, is proposed to be responsible for the degradation of cyclohexane. Quantitative growth experiments showed that cyclohexane degradation was coupled with the stoichiometric reduction of sulfate to sulfide. Substrate response tests corroborated with hybridization with a sequence-specific oligonucleotide probe suggested that the dominant phylotype apparently was able to degrade other cyclic and n-alkanes, including the gaseous alkane n-butane. Based on GC-MS analyses of culture extracts cyclohexylsuccinate was identified as a metabolite, indicating an activation of cyclohexane by addition to fumarate. Other metabolites detected were 3-cyclohexylpropionate and cyclohexanecarboxylate providing evidence that the overall degradation pathway of cyclohexane under anoxic conditions is analogous to that of n-alkanes.

Phenotypic switching in bacteria

NASA Astrophysics Data System (ADS)

Merrin, Jack

Living matter is a non-equilibrium system in which many components work in parallel to perpetuate themselves through a fluctuating environment. Physiological states or functionalities revealed by a particular environment are called phenotypes. Transitions between phenotypes may occur either spontaneously or via interaction with the environment. Even in the same environment, genetically identical bacteria can exhibit different phenotypes of a continuous or discrete nature. In this thesis, we pursued three lines of investigation into discrete phenotypic heterogeneity in bacterial populations: the quantitative characterization of the so-called bacterial persistence, a theoretical model of phenotypic switching based on those measurements, and the design of artificial genetic networks which implement this model. Persistence is the phenotype of a subpopulation of bacteria with a reduced sensitivity to antibiotics. We developed a microfluidic apparatus, which allowed us to monitor the growth rates of individual cells while applying repeated cycles of antibiotic treatments. We were able to identify distinct phenotypes (normal and persistent) and characterize the stochastic transitions between them. We also found that phenotypic heterogeneity was present prior to any environmental cue such as antibiotic exposure. Motivated by the experiments with persisters, we formulated a theoretical model describing the dynamic behavior of several discrete phenotypes in a periodically varying environment. This theoretical framework allowed us to quantitatively predict the fitness of dynamic populations and to compare survival strategies according to environmental time-symmetries. These calculations suggested that persistence is a strategy used by bacterial populations to adapt to fluctuating environments. Knowledge of the phenotypic transition rates for persistence may provide statistical information about the typical environments of bacteria. We also describe a design of artificial

Food deprivation and prior anoxic coma have opposite effects on the activity of a visual interneuron in the locust.

PubMed

Cross, Kevin P; Britton, Samantha; Mangulins, Rebecca; Money, Tomas G A; Robertson, R Meldrum

2017-04-01

We compared how different metabolic stressors, anoxic coma and food deprivation, affected signaling in neural tissue. We used the locust's Descending Contralateral Movement Detector (DCMD) interneuron because its large axon, high firing frequencies, and rapid conduction velocity make it energetically expensive. We exposed locusts to a 30min anoxic coma or 1day of food deprivation and found contrasting effects on signaling within the axon. After a prior anoxic coma, the DCMD fired fewer high-frequency (>200Hz) action potentials (APs) (Control: 12.4±1.6; Coma: 6.3±0.9) with a reduction in axonal conduction velocity (CV) at all frequencies (∼4-8%) when presented with a standard looming visual stimulus. Prior anoxic coma was also associated with a loss of supernormal conduction by reducing both the number of supernormal APs and the firing frequency with the highest CV. Initially, food deprivation caused a significant increase in the number of low- and high-frequency APs with no differences observed in CV. After controlling for isolation, food deprivation resulted in an increase in high-frequency APs (>200Hz: Control: 17.1±1.7; Food-deprived: 19.9±1.3) and an increase in relative conduction velocity for frequencies >150Hz (∼2%). Action potentials of food-deprived animals had a smaller half-width (Control: 0.45±0.02ms; Food-deprived: 0.40±0.01ms) and decay time (Control: 0.62±0.03ms; Food-deprived: 0.54±0.02ms). Our data indicate that the effects of metabolic stress on neural signaling can be stressor-dependent. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dynamic interplay between microbial denitrification and antibiotic resistance under enhanced anoxic denitrification condition in soil.

PubMed

Sun, Mingming; Ye, Mao; Liu, Kuan; Schwab, Arthur P; Liu, Manqiang; Jiao, Jiaguo; Feng, Yanfang; Wan, Jinzhong; Tian, Da; Wu, Jun; Li, Huixin; Hu, Feng; Jiang, Xin

2017-03-01

Mixed contamination of nitrate and antibiotics/antibiotic-resistant genes (ARGs) is an emerging environmental risk to farmland soil. This is the first study to explore the role of excessive anthropogenic nitrate input in the anoxic dissipation of soil antibiotic/ARGs. During the initial 10 days of incubation, the presence of soil antibiotics significantly inhibited NO 3 - dissipation, N 2 O production rate, and denitrifying genes (DNGs) abundance in soil (p < 0.05). Between days 10 and 30, by contrast, enhanced denitrification clearly prompted the decline in antibiotic contents and ARG abundance. Significantly negative correlations were detected between DNGs and ARGs, suggesting that the higher the DNG activity, the more dramatic is the denitrification and the greater are the antibiotic dissipation and ARG abundance. This study provides crucial knowledge for understanding the mutual interaction between soil DNGs and ARGs in the enhanced anoxic denitrification condition. Copyright © 2016 Elsevier Ltd. All rights reserved.

Define of internal recirculation coefficient for biological wastewater treatment in anoxic and aerobic bioreactors

NASA Astrophysics Data System (ADS)

Rossinskyi, Volodymyr

2018-02-01

The biological wastewater treatment technologies in anoxic and aerobic bioreactors with recycle of sludge mixture are used for the effective removal of organic compounds from wastewater. The change rate of sludge mixture recirculation between bioreactors leads to a change and redistribution of concentrations of organic compounds in sludge mixture in bioreactors and change hydrodynamic regimes in bioreactors. Determination of the coefficient of internal recirculation of sludge mixture between bioreactors is important for the choice of technological parameters of biological treatment (wastewater treatment duration in anoxic and aerobic bioreactors, flow capacity of recirculation pumps). Determination of the coefficient of internal recirculation of sludge mixture requires integrated consideration of hydrodynamic parameter (flow rate), kinetic parameter (rate of oxidation of organic compounds) and physical-chemical parameter of wastewater (concentration of organic compounds). The conducted numerical experiment from the proposed mathematical equations allowed to obtain analytical dependences of the coefficient of internal recirculation sludge mixture between bioreactors on the concentration of organic compounds in wastewater, the duration of wastewater treatment in bioreactors.

Mycorrhiza helper bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deveau, Aurelie; Labbe, Jessy

This chapter focuses on the Mycorrhiza Helper Bacteria (MHB), a generic name given to bacteria which stimulate the formation of mycorrhizal symbiosis. By extension, some bacterial strains that positively impact the functioning of mycorrhizal symbiosis are also called MHB. These bacteria have applicative interests, as they indirectly improve the health and growth of tree seedlings. MHB are not restricted to a specific type of ecosystem, but are rather generalist in the way that they associate with both herbaceous and woody mycorrhizal plants from boreal, temperate, arid and tropical ecosystems. However, understanding the molecular mechanisms and their specificities will help usmore » to know more about the ecology of the MHB. The process of acquisition varies between fungal species; while ectomycorrhizal fungi most probably recurrently acquire them from the environment, the association between bacterial endosymbionts and Glomeromycota probably dates back to very ancient times, and has since been vertically transmitted.« less

Interactions between Diatoms and Bacteria

PubMed Central

Amin, Shady A.; Parker, Micaela S.

2012-01-01

Summary: Diatoms and bacteria have cooccurred in common habitats for hundreds of millions of years, thus fostering specific associations and interactions with global biogeochemical consequences. Diatoms are responsible for one-fifth of the photosynthesis on Earth, while bacteria remineralize a large portion of this fixed carbon in the oceans. Through their coexistence, diatoms and bacteria cycle nutrients between oxidized and reduced states, impacting bioavailability and ultimately feeding higher trophic levels. Here we present an overview of how diatoms and bacteria interact and the implications of these interactions. We emphasize that heterotrophic bacteria in the oceans that are consistently associated with diatoms are confined to two phyla. These consistent bacterial associations result from encounter mechanisms that occur within a microscale environment surrounding a diatom cell. We review signaling mechanisms that occur in this microenvironment to pave the way for specific interactions. Finally, we discuss known interactions between diatoms and bacteria and exciting new directions and research opportunities in this field. Throughout the review, we emphasize new technological advances that will help in the discovery of new interactions. Deciphering the languages of diatoms and bacteria and how they interact will inform our understanding of the role these organisms have in shaping the ocean and how these interactions may change in future oceans. PMID:22933565

Inorganic mercury binding with different sulfur species in anoxic sediments and their gut juice extractions.

PubMed

Zhong, Huan; Wang, Wen-Xiong

2009-09-01

To investigate the roles of different sulfur (S) species in controlling the partitioning and bioavailability of inorganic mercury (Hg) in anoxic sediments, we examined the differential binding of Hg with three key S species in anoxic sediment (mackinawite [FeS], pyrite [FeS2], and S(2-)) and then quantified their extraction by the gut juice of deposit-feeding sipunculans Sipunculus nudus. A sequential extraction method was simultaneously used to distinguish Hg sorption with different sediment components. All three S-containing sediment components could lead to a high binding of Hg in sediments, but most Hg was sorbed with FeS or FeS2 instead of formation of Hg sulfide despite the presence of S(2-) or humic acid. The gut juice extraction was relatively low and constant whenever FeS and FeS2 were in the sediment, indicating that both FeS and FeS2 controlled the Hg gut juice extraction and thus bioavailability. Mercury sorbed with FeS2 had higher gut juice extraction than that with FeS, while Hg sulfide was not extracted, strongly suggesting that Hg sorbed with FeS2 was more bioavailable than that with other S species. Mercury sorbed with FeS had very low bioavailability to sipunculans at a low Hg:S ratio in the sediment but was more bioavailable with increasing Hg:S ratio up to a maximum (approximately 1:10, mole based). The present study showed that different S species (FeS, FeS2) and Hg:S ratios significantly affected the binding and bioavailability of Hg in anoxic sediments.

Process for generation of hydrogen gas from various feedstocks using thermophilic bacteria

DOEpatents

Ooteghem, Suellen Van

2005-09-13

A method for producing hydrogen gas is provided comprising selecting a bacteria from the Order Thermotogales, subjecting the bacteria to a feedstock and to a suitable growth environment having an oxygen concentration below the oxygen concentration of water in equilibrium with air; and maintaining the environment at a predetermined pH and at a temperature of at least approximately 45.degree. C. for a time sufficient to allow the bacteria to metabolize the feedstock.

Schwertmannite stability in anoxic Fe(II)-rich aqueous solution

NASA Astrophysics Data System (ADS)

Paikaray, Susanta; Schröder, Christian; Peiffer, Stefan

2017-11-01

Schwertmannite (SHM) is a powerful scavenger for As(III) leading to As(III)-enriched precipitates around acid mine drainage environments that may become exposed to aqueous Fe(II). In this study we have investigated the stability of pure SHM and SHM containing 0.92 wt% As(III) under Fe(II)aq-rich (0.4-1.0 mM) anoxic conditions using XRD, SEM, Mössbauer and FTIR spectroscopic techniques. Schwertmannite transformation proceeded through an alkalinity-driven pathway releasing sulfate and a Fe(II)-catalyzed pathway that generated lepidocrocite and goethite at pH 6 and 6.9 in the presence of 1 mM Fe(II)aq. Lepidocrocite was found to be needle shaped if the SHM contained As(III) and platy for pure SHM. Goethite had a poor degree of crystallinity in As(III) containing SHM. Pre-adsorption of As(III) inhibited the extent of SHM transformation. Fe(II) sorption onto SHM was pH dependent and reflected a sorption edge with complete consumption at pH 6.9, while only ∼20% were adsorbed at pH 5. Surface coverage with Fe(II) appears to be the key parameter controlling extent and products of the transformation process. As(III) concentrations in solution are controlled by two mechanisms: (1) exchange of As(III) for sulfate upon alkalinity-driven transformation of schwertmannite and (2) re-adsorption to new phases formed upon Fe(II)-catalyzed transformation. The adsorbed As(III) has inhibited the extent of transformation and was partly released with the maximum release at pH 5 (0.5%) in the absence of Fe(II)aq.

Electric coupling between distant nitrate reduction and sulfide oxidation in marine sediment

PubMed Central

Marzocchi, Ugo; Trojan, Daniela; Larsen, Steffen; Louise Meyer, Rikke; Peter Revsbech, Niels; Schramm, Andreas; Peter Nielsen, Lars; Risgaard-Petersen, Nils

2014-01-01

Filamentous bacteria of the Desulfobulbaceae family can conduct electrons over centimeter-long distances thereby coupling oxygen reduction at the surface of marine sediment to sulfide oxidation in deeper anoxic layers. The ability of these cable bacteria to use alternative electron acceptors is currently unknown. Here we show that these organisms can use also nitrate or nitrite as an electron acceptor thereby coupling the reduction of nitrate to distant oxidation of sulfide. Sulfidic marine sediment was incubated with overlying nitrate-amended anoxic seawater. Within 2 months, electric coupling of spatially segregated nitrate reduction and sulfide oxidation was evident from: (1) the formation of a 4–6-mm-deep zone separating sulfide oxidation from the associated nitrate reduction, and (2) the presence of pH signatures consistent with proton consumption by cathodic nitrate reduction, and proton production by anodic sulfide oxidation. Filamentous Desulfobulbaceae with the longitudinal structures characteristic of cable bacteria were detected in anoxic, nitrate-amended incubations but not in anoxic, nitrate-free controls. Nitrate reduction by cable bacteria using long-distance electron transport to get privileged access to distant electron donors is a hitherto unknown mechanism in nitrogen and sulfur transformations, and the quantitative importance for elements cycling remains to be addressed. PMID:24577351

Protist-Bacteria Associations: Gammaproteobacteria and Alphaproteobacteria Are Prevalent as Digestion-Resistant Bacteria in Ciliated Protozoa

PubMed Central

Gong, Jun; Qing, Yao; Zou, Songbao; Fu, Rao; Su, Lei; Zhang, Xiaoli; Zhang, Qianqian

2016-01-01

Protistan bacterivory, a microbial process involving ingestion and digestion, is ecologically important in the microbial loop in aquatic and terrestrial ecosystems. While bacterial resistance to protistan ingestion has been relatively well understood, little is known about protistan digestion in which some ingested bacteria could not be digested in cells of major protistan grazers in the natural environment. Here we report the phylogenetic identities of digestion-resistant bacteria (DRB) that could survive starvation and form relatively stable associations with 11 marine and one freshwater ciliate species. Using clone library and sequencing of 16S rRNA genes, we found that the protistan predators could host a high diversity of DRB, most of which represented novel bacterial taxa that have not been cultivated. The localization inside host cells, quantity, and viability of these bacteria were checked using fluorescence in situ hybridization. The DRB were affiliated with Actinobacteria, Bacteroidetes, Firmicutes, Parcubacteria (OD1), Planctomycetes, and Proteobacteria, with Gammaproteobacteria and Alphaproteobacteria being the most frequently occurring classes. The dominance of Gamma- and Alphaproteobacteria corresponds well to a previous study of Global Ocean Sampling metagenomic data showing the widespread types of bacterial type VI and IV secretion systems (T6SS and T4SS) in these two taxa, suggesting a putatively significant role of secretion systems in promoting marine protist-bacteria associations. In the DRB assemblages, opportunistic bacteria such as Alteromonadaceae, Pseudoalteromonadaceae, and Vibrionaceae often presented with high proportions, indicating these bacteria could evade protistan grazing thus persist and accumulate in the community, which, however, contrasts with their well-known rarity in nature. This begs the question whether viral lysis is significant in killing these indigestible bacteria in microbial communities. Taken together, our study on

Fate and transport of bacteria injected into aquifers

USGS Publications Warehouse

Harvey, Ronald W.

1993-01-01

Advances in our understanding of the fate and transport of bacteria introduced into aquifers, including the potential use of genetically engineered bacteria for biorestoration, are highlighted by new findings in the following areas: modeling of bacterial attachment during transport through porous media, the long-term survival of a chlorobenzoate-degrading bacterium injected into a contaminated sandy aquifer, and molecular techniques that may be used in tracking genetically engineered bacteria in groundwater environments.

Multi-proxy study of Ocean Anoxic Event 2 (Cenomanian-Turonian) yields new perspective on the drivers for Mesozoic anoxic events

NASA Astrophysics Data System (ADS)

Sageman, B. B.; Hurtgen, M.; Jacobson, A. D.; Selby, D. S.

2015-12-01

Mesozoic ocean anoxic events have long been a focus of intense study because they appear to reflect a large-scale oscillation of the marine redox state from oxic to anoxic, and at least locally sulfidic. The consensus view on the cause of these events has changed over the past 39 years, since they were first defined. A global net increase in primary production is now widely accepted as the key driver, and the evidence for a volcanic trigger of this process is strong. However, the exact pathway from volcanism to OAE is less certain. Some authors favor the direct role of a massive load of reduced compounds in LIP hydrothermal fluxes for consuming available marine oxygen. Others prefer the indirect pathway of oxygen consumption by enhanced organic matter flux, which requires a major increase in nutrient budgets. Metallic micronutrients in the hydrothermal fluxes have been hypothesized, as have increases in riverine phosphorus fluxes due to enhanced weathering that would result from volcanic CO2 driven warming. Our recent work on the OAE2 interval has led to some new ideas about these hypothesized drivers. In particular, refinement of the Late Cenomanian time scale, and comparison of the geochemical records of d13C, d34S, Osi, P phases, and d44Ca between selected sections in North America and Europe has suggested the following sequence of events: 1) Osi data indicate that the onset of a major volcanic event precedes the positive shift in C-isotopes by at least 40 to possibly 180 kyr; 2) a positive shift in d44Ca data interpreted to indicate ocean acidification is coincident with the volcanic event; 3) the positive shift in C-isotopes is interpreted to reflect the accumulated burial of marine organic matter sufficient to shift the C-reservoir to heavier values; thus, our data suggest that up to 180 kyr was required for the shift in nutrient supply, productivity increase, and organic matter burial. Two mechanisms that conceivably match the lagged character of the event

Regulating the Intersection of Metabolism and Pathogenesis in Gram-positive Bacteria

PubMed Central

RICHARDSON, ANTHONY R.; SOMERVILLE, GREG A.; SONENSHEIN, ABRAHAM L.

2015-01-01

Pathogenic bacteria must contend with immune systems that actively restrict the availability of nutrients and cofactors, and create a hostile growth environment. To deal with these hostile environments, pathogenic bacteria have evolved or acquired virulence determinants that aid in the acquisition of nutrients. This connection between pathogenesis and nutrition may explain why regulators of metabolism in nonpathogenic bacteria are used by pathogenic bacteria to regulate both metabolism and virulence. Such coordinated regulation is presumably advantageous because it conserves carbon and energy by aligning synthesis of virulence determinants with the nutritional environment. In Gram-positive bacterial pathogens, at least three metabolite-responsive global regulators, CcpA, CodY, and Rex, have been shown to coordinate the expression of metabolism and virulence genes. In this chapter, we discuss how environmental challenges alter metabolism, the regulators that respond to this altered metabolism, and how these regulators influence the host-pathogen interaction. PMID:26185086

Evaluating the microbial community and gene regulation involved in crystallization kinetics of ZnS formation in reduced environments

NASA Astrophysics Data System (ADS)

Falk, Nicholas; Chaganti, Subba Rao; Weisener, Christopher G.

2018-01-01

In anoxic environments, sulfate-reducing bacteria (SRB) may precipitate sparingly-soluble, fine-grained sulfides as by-products of dissimilatory sulfate reduction. This bio-mechanism lends importance to acid rock drainage (ARD) remediation efforts for its ability to immobilize harmful metals from contaminant pathways, including Zn. However, SRB often coexist alongside multiple bacterial guilds in these environments, and may be sustained or hindered by the activities and metabolic by-products of their cohorts, driven by the commonly available substrates. Thus, the effectiveness of onset sulfate reduction and resultant metal-sulfide generation in ARD treatment can be enhanced by unravelling the complexities associated with these interactions. This research used material sourced from a passive bioreactor system located at the Stockton Coal Mine, New Zealand to investigate SRB activity and associated community function. RNA sequencing showed spore-forming Desulfitobacterium and Desulfotomaculum as the dominant SRB enriched from the reduced zone of the bioreactor. Metatranscriptomic analysis revealed acetogenic bacteria as syntrophic partners in substrate availability and Pseudomonas as metal-resistant community members. ZnS precipitates were observed by scanning electron microscopy (SEM) in short-term batch enrichments as well as long-term raw bioreactor material, with observed differences in mineral arrangement indicative of different nucleation scenarios. Syntrophy, metal response mechanisms, and the capacity for sporulation were observed as key microbial functions in mine waste reclamation settings. Here, Zn and S mass balance calculations coupled with RNA sequence data and microscopy illuminated favourable physicochemical and biological conditions for early metal sulfide precipitation in passive treatment systems for ARD and highlight the advantages of linking both lab and field-scale studies.

Strategies and ecological roles of algicidal bacteria.

PubMed

Meyer, Nils; Bigalke, Arite; Kaulfuß, Anett; Pohnert, Georg

2017-11-01

In both freshwater and marine ecosystems, phytoplankton are the most dominant primary producers, contributing substantially to aquatic food webs. Algicidal bacteria that can associate to microalgae from the phytoplankton have the capability to control the proliferation and even to lyse them. These bacteria thus play an important role in shaping species composition in pelagic environments. In this review, we discuss and categorise strategies used by algicidal bacteria for the attack on microalgae. We highlight the complex regulation of algicidal activity and defence responses that govern alga-bacteria interactions. We also discuss how algicidal bacteria impact algal physiology and metabolism and survey the existing algicidal metabolites and enzymes. The review illustrates that the ecological role of algicidal bacteria is not yet fully understood and critically discusses the challenges in obtaining ecologically relevant data. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Evidence for abiotic sulfurization of marine dissolved organic matter in sulfidic environments

NASA Astrophysics Data System (ADS)

Pohlabeln, A. M.; Niggemann, J.; Dittmar, T.

2016-02-01

Sedimentary organic matter abiotically sulfurizes in sulfidic marine environments. Here we hypothesize that sulfurization also affects dissolved organic matter (DOM), and that sulfidic marine environments are sources of dissolved organic sulfur (DOS) to the ocean. To test these hypotheses we studied solid-phase extractable (SPE) DOS in the Black Sea at various water column depths (oxic and anoxic) and in sediment porewaters from the German Wadden Sea. The concentration and molecular composition of SPE-DOS from these sites and from the oxic water columns of the North Sea (Germany) and of the North Pacific were compared. In support of our hypotheses, SPE-DOS concentrations were elevated in sulfidic waters compared to oxic waters. For a detailed molecular characterization of SPE-DOS, selective wet-chemical alteration experiments targeting different sulfur-containing functional groups were applied prior to Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). These experiments included harsh hydrolysis, selective derivatization of thiols, oxidation, and deoxygenation to test for thioesters, sulfonic acid esters, alkylsulfates, thiols, non-aromatic thioethers, and sulfoxides. Additionally, collision-induced fragmentation experiments were applied to test for sulfonic acids. The tests revealed that the sulfonic acid group was the main structural feature in SPE-DOS, independent of the environmental conditions of the sampling site. Only in Wadden Sea anoxic porewater also non-aromatic thioethers were found which are presumably not stable in oxic waters. The findings from our field studies were confirmed in laboratory experiments, where we abiotically sulfurized marine and algal-derived DOM under conditions similar to that in anoxic marine sediments.

Monitoring of airborne bacteria and aerosols in different wards of hospitals - Particle counting usefulness in investigation of airborne bacteria.

PubMed

Mirhoseini, Seyed Hamed; Nikaeen, Mahnaz; Khanahmd, Hossein; Hatamzadeh, Maryam; Hassanzadeh, Akbar

2015-01-01

The presence of airborne bacteria in hospital environments is of great concern because of their potential role as a source of hospital-acquired infections (HAI). The aim of this study was the determination and comparison of the concentration of airborne bacteria in different wards of four educational hospitals, and evaluation of whether particle counting could be predictive of airborne bacterial concentration in different wards of a hospital. The study was performed in an operating theatre (OT), intensive care unit (ICU), surgery ward (SW) and internal medicine (IM) ward of four educational hospitals in Isfahan, Iran. A total of 80 samples were analyzed for the presence of airborne bacteria and particle levels. The average level of bacteria ranged from 75-1194 CFU/m (3) . Mean particle levels were higher than class 100,000 cleanrooms in all wards. A significant correlation was observed between the numbers of 1-5 µm particles and levels of airborne bacteria in operating theatres and ICUs. The results showed that factors which may influence the airborne bacterial level in hospital environments should be properly managed to minimize the risk of HAIs especially in operating theaters. Microbial air contamination of hospital settings should be performed by the monitoring of airborne bacteria, but particle counting could be considered as a good operative method for the continuous monitoring of air quality in operating theaters and ICUs where higher risks of infection are suspected.

Genetic basis and importance of metal resistant genes in bacteria for bioremediation of contaminated environments with toxic metal pollutants.

PubMed

Das, Surajit; Dash, Hirak R; Chakraborty, Jaya

2016-04-01

Metal pollution is one of the most persistent and complex environmental issues, causing threat to the ecosystem and human health. On exposure to several toxic metals such as arsenic, cadmium, chromium, copper, lead, and mercury, several bacteria has evolved with many metal-resistant genes as a means of their adaptation. These genes can be further exploited for bioremediation of the metal-contaminated environments. Many operon-clustered metal-resistant genes such as cadB, chrA, copAB, pbrA, merA, and NiCoT have been reported in bacterial systems for cadmium, chromium, copper, lead, mercury, and nickel resistance and detoxification, respectively. The field of environmental bioremediation has been ameliorated by exploiting diverse bacterial detoxification genes. Genetic engineering integrated with bioremediation assists in manipulation of bacterial genome which can enhance toxic metal detoxification that is not usually performed by normal bacteria. These techniques include genetic engineering with single genes or operons, pathway construction, and alternations of the sequences of existing genes. However, numerous facets of bacterial novel metal-resistant genes are yet to be explored for application in microbial bioremediation practices. This review describes the role of bacteria and their adaptive mechanisms for toxic metal detoxification and restoration of contaminated sites.

Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones.

PubMed

Peng, Xuefeng; Jayakumar, Amal; Ward, Bess B

2013-01-01

Ammonia-oxidizing archaea (AOA) have been reported at high abundance in much of the global ocean, even in environments, such as pelagic oxygen minimum zones (OMZs), where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA). The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP) AOA assemblages was investigated using principal component analysis (PCA) and redundancy analysis (RDA). In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature (higher in the Arabian Sea than in the ETSP) was the main factor that correlated with the differences between the AOA communities. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role, than did geography, in shaping the AOA community composition.

Kinetics and isotherm analysis of 2,4-dichlorophenoxyl acetic acid adsorption onto soil components under oxic and anoxic conditions.

PubMed

Ololade, Isaac A; Alomaja, Folasade; Oladoja, Nurudeen A; Ololade, Oluwaranti O; Oloye, Femi F

2015-01-01

2,4-dichlorophenoxyl acetic acid (2,4-D, pKa = 2.8) is used extensively as a herbicide in agricultural practices. Its sorption behavior on both untreated and soils treated to significantly remove specific components (organic and iron and manganese [Fe-Mn] oxides and hydroxides phases) was investigated under oxic and anoxic conditions. The chemical and structural heterogeneity of the soil components were characterized by elemental analysis and X-ray diffraction (XRD). The coexistence of the various components seems to either mask sorption sites on the untreated soil surfaces or inhibit interlayer diffusion of 2,4-D. All sorption data conform to the Freundlich description and a pseudo-second-order kinetic model. There was a strong positive correlation between sorption capacity K(d), and surface area (r(2) ≤ 0.704), but a negative correlation was uncovered with both pH and organic carbon (r(2) ≤ -0.860). The results indicate that 2,4-D is preferably sorbed under oxic rather than anoxic conditions and it is greater on soils containing a high Fe content. There was incomplete 2,4-D sorption reversibility, with desorption occurring more rapidly under anoxic conditions. The study suggests that stimulation of Fe III reduction could be used for the bioremediation of a 2,4-D-contaminated site.

Unraveling the potential of a combined nitritation-anammox biomass towards the biodegradation of pharmaceutically active compounds.

PubMed

Kassotaki, Elissavet; Pijuan, Maite; Joss, Adriano; Borrego, Carles M; Rodriguez-Roda, Ignasi; Buttiglieri, Gianluigi

2018-05-15

In the past few years, anaerobic ammonium oxidation-based processes have attracted a lot of attention for their implementation at the mainstream line of wastewater treatment plants, due to the possibility of leading to energy autarky if combined with anaerobic digestion. However, little is known about the potential degradation of micropollutants by the microbial groups responsible of these processes and the few results available are inconclusive. This study aimed to assess the degradation capability of biomass withdrawn from a combined nitritation/anaerobic ammonium oxidation (combined N/A) pilot plant towards five pharmaceutically active compounds (ibuprofen, sulfamethoxazole, metoprolol, venlafaxine and carbamazepine). Batch experiments were performed under different conditions by selectively activating or inhibiting different microbial groups: i) regular combined N/A operation, ii) aerobic (optimal for nitrifying bacteria), iii) aerobic with allylthiourea (an inhibitor of ammonia monooxygenase, enzyme of ammonia oxidizing bacteria), iv) anoxic (optimal for anaerobic ammonium oxidizing bacteria), v) aerobic with acetate (optimal for heterotrophic bacteria) and vi) anoxic with acetate (optimal for heterotrophic denitrifying bacteria). Ibuprofen was the most biodegradable compound being significantly degraded (49-100%) under any condition except heterotrophic denitrification. Sulfamethoxazole, exhibited the highest removal (70%) under optimal conditions for nitrifying bacteria but in the rest of the experiments anoxic conditions were found to be slightly more favorable (up to 58%). For metoprolol the highest performance was obtained under anoxic conditions favoring anammox bacteria (62%). Finally, carbamazepine and venlafaxine were hardly removed (≤10% in the majority of cases). Taken together, these results suggest the specificity of different microbial groups that in combination with alternating operational parameters can lead to enhanced removal of some

The Role of Plant Growth-Promoting Bacteria in Metal Phytoremediation.

PubMed

Kong, Zhaoyu; Glick, Bernard R

2017-01-01

Phytoremediation is a promising technology that uses plants and their associated microbes to clean up contaminants from the environment. In recent years, phytoremediation assisted by plant growth-promoting bacteria (PGPB) has been highly touted for cleaning up toxic metals from soil. PGPB include rhizospheric bacteria, endophytic bacteria and the bacteria that facilitate phytoremediation by other means. This review provides information about the traits and mechanisms possessed by PGPB that improve plant metal tolerance and growth, and illustrate mechanisms responsible for plant metal accumulation/translocation in plants. Several recent examples of phytoremediation of metals facilitated by PGPB are reviewed. Although many encouraging results have been reported in the past years, there have also been numerous challenges encountered in phytoremediation in the field. To implement PGPB-assisted phytoremediation of metals in the natural environment, there is also a need to critically assess the ecological effects of PGPB, especially for those nonnative bacteria. © 2017 Elsevier Ltd All rights reserved.

Freshwater bacteria release methane as a byproduct of phosphorus acquisition.

PubMed

Yao, Mengyin; Henny, Cynthia; Maresca, Julia A

2016-09-30

Freshwater lakes emit large amounts of methane, some of which is produced in oxic surface waters. Two potential pathways for aerobic methane production exist: methanogenesis in oxygenated water, which has been observed in some lakes, or demethylation of small organic molecules. Although methane is produced via demethylation in oxic marine environments, this mechanism of methane release has not yet been demonstrated in freshwater systems. Genes related to the C-P lyase pathway, which cleaves C-P bonds in phosphonate compounds, were found in a metagenomic survey of the surface water of Lake Matano, which is chronically P-starved and methane-rich. We demonstrate that four bacterial isolates from Lake Matano obtain P from methylphosphonate and release methane, and that this activity is repressed by phosphate. We further demonstrate that expression of phnJ, which encodes the enzyme that releases methane, is higher in the presence of methylphosphonate and lower when both methylphosphonate and phosphate are added. This gene is also found in most of the metagenomic data sets from freshwater environments. These experiments link methylphosphonate degradation and methane production with gene expression and phosphate availability in freshwater organisms, and suggest that some of the excess methane in the Lake Matano surface water, and in other methane-rich lakes, may be produced by P-starved bacteria. Methane is an important greenhouse gas, and contributes substantially to global warming. Although freshwater environments are known to release methane into the atmosphere, estimates of the amount of methane emitted by freshwater lakes vary from 8 to 73 Tg per year. Methane emissions are difficult to predict in part because the source of the methane can vary: it is the end product of the energy-conserving pathway in methanogenic archaea, which predominantly live in anoxic sediments or waters, but have also been identified in some oxic freshwater environments. More recently

Drought-Tolerance of Wheat Improved by Rhizosphere Bacteria from Harsh Environments: Enhanced Biomass Production and Reduced Emissions of Stress Volatiles

PubMed Central

Timmusk, Salme; Abd El-Daim, Islam A.; Copolovici, Lucian; Tanilas, Triin; Kännaste, Astrid; Behers, Lawrence; Nevo, Eviatar; Seisenbaeva, Gulaim; Stenström, Elna; Niinemets, Ülo

2014-01-01

Water is the key resource limiting world agricultural production. Although an impressive number of research reports have been published on plant drought tolerance enhancement via genetic modifications during the last few years, progress has been slower than expected. We suggest a feasible alternative strategy by application of rhizospheric bacteria coevolved with plant roots in harsh environments over millions of years, and harboring adaptive traits improving plant fitness under biotic and abiotic stresses. We show the effect of bacterial priming on wheat drought stress tolerance enhancement, resulting in up to 78% greater plant biomass and five-fold higher survivorship under severe drought. We monitored emissions of seven stress-related volatiles from bacterially-primed drought-stressed wheat seedlings, and demonstrated that three of these volatiles are likely promising candidates for a rapid non-invasive technique to assess crop drought stress and its mitigation in early phases of stress development. We conclude that gauging stress by elicited volatiles provides an effectual platform for rapid screening of potent bacterial strains and that priming with isolates of rhizospheric bacteria from harsh environments is a promising, novel way to improve plant water use efficiency. These new advancements importantly contribute towards solving food security issues in changing climates. PMID:24811199

Metabolic behavior and enzymatic aspects of denitrifying EBPR sludge in a continuous-flow anaerobic-anoxic system.

PubMed

Zafiriadis, Ilias; Ntougias, Spyridon; Kapagiannidis, Anastasios G; Aivasidis, Alexander

2013-10-01

The metabolic aspects of enhanced biological phosphorus removal (EBPR) were investigated for the first time in a continuous-flow anaerobic-anoxic plant fed with acetate, propionate, or substrates which are involved in the tricarboxylic acid and/or glyoxylate cycle, i.e., fumarate, malate, or oxaloacetate, as the sole carbon source. Although the polyphosphate-accumulating organisms (PAOs) population remained stable with any carbon source examined, no typical EBPR metabolism was observed during fumarate, malate, or oxaloacetate utilization. Specific enzymatic activities related to EBPR were determined in activated sludge homogenates and directly correlated with the nutrient metabolic rates. The experimental results indicated the direct involvement of alkaline phosphatase, pyrophosphatase, and exopolyphosphatase in the denitrifying EBPR process. Metabolic aspects of glyoxylate cycle enzymes are discussed with regard to the biomass anaerobic and anoxic activity. Process performance was highly influenced by the kind of substrate utilized, indicating that specific metabolic pathways should be followed to favor efficient EBPR.

Public health significance of antimicrobial-resistant gram-negative bacteria in raw bulk tank milk.

PubMed

Straley, B A; Donaldson, S C; Hedge, N V; Sawant, A A; Srinivasan, V; Oliver, S P; Jayarao, B M

2006-01-01

The dairy farm environment and animals on the farm serve as important reservoirs of pathogenic and commensal bacteria that could potentially gain access to milk in the bulk tank via several pathways. Pathogenic gram-negative bacteria can gain access to bulk tank milk from infected mammary glands, contaminated udders and milking machines, and/or from the dairy farm environment. Contaminated raw milk when consumed by humans or fed to animals on the farm can result in gastroenteric infections in humans and animals and also provide an opportunity for organisms to colonize the farm environment. This scenario becomes much more complicated when pathogenic bacteria such as Salmonella, Shiga toxin-producing Escherichia coli, and commensal gram-negative enteric bacteria encode for antimicrobial resistance determinants. In recent years, the role of commensal bacteria as reservoirs of genetic determinants for antimicrobial resistance has come under closer scrutiny. Commensal bacteria in bulk tank milk can be a significant reservoir of antimicrobial determinants. Raw milk consumption can result in exposure to antimicrobial-resistant commensal gram-negative bacteria. This paper examines the prevalence and role of commensal gram-negative enteric bacteria in bulk tank milk and their public health significance.

Sulfur-Oxidizing Bacteria in Soap Lake (Washington State), a Meromictic, Haloalkaline Lake with an Unprecedented High Sulfide Content▿

PubMed Central

Sorokin, Dimitry Y.; Foti, Mirjam; Pinkart, Holly C.; Muyzer, Gerard

2007-01-01

Culture-dependent and -independent techniques were used to study the diversity of chemolithoautotrophic sulfur-oxidizing bacteria in Soap Lake (Washington State), a meromictic, haloalkaline lake containing an unprecedentedly high sulfide concentration in the anoxic monimolimnion. Both approaches revealed the dominance of bacteria belonging to the genus Thioalkalimicrobium, which are common inhabitants of soda lakes. A dense population of Thioalkalimicrobium (up to 107 cells/ml) was found at the chemocline, which is characterized by a steep oxygen-sulfide gradient. Twelve Thioalkalimicrobium strains exhibiting three different phenotypes were isolated in pure culture from various locations in Soap Lake. The isolates fell into two groups according to 16S rRNA gene sequence analysis. One of the groups was closely related to T. cyclicum, which was isolated from Mono Lake (California), a transiently meromictic, haloalkaline lake. The second group, consisting of four isolates, was phylogenetically and phenotypically distinct from known Thioalkalimicrobium species and unique to Soap Lake. It represented a new species, for which we suggest the name Thioalkalimicrobium microaerophilum sp. nov. PMID:17114324

Use of thermophilic bacteria for bioremediation of petroleum contaminants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Al-Maghrabi, I.M.A.; Bin Aqil, A.O.; Chaalal, O.

1999-01-01

Several strains of thermophilic bacteria were isolated from the environment of the United Arab Emirates. These bacteria show extraordinary resistance to heat and have their maximum growth rate around 60--80 C. This article investigates the potential of using these facultative bacteria for both in situ and ex situ bioremediation of petroleum contaminants. In a series of batch experiments, bacterial growth was observed using a computer image analyzer following a recently developed technique. These experiments showed clearly that the growth rate is enhanced in the presence of crude oil. This is coupled with a rapid degradation of the crude oil. Thesemore » bacteria were found to be ideal for breaking down long-chain organic molecules at a temperature of 40 C, which is the typical ambient temperature of the Persian Gulf region. The same strains of bacteria are also capable of surviving in the presence of the saline environment that can prevail in both sea water and reservoir connate water. This observation prompted further investigation into the applicability of the bacteria in microbial enhanced oil recovery. In the United Arab Emirates, the reservoirs are typically at a temperature of around 85 C. Finally, the performance of the bacteria is tested in a newly developed bioreactor that uses continuous aeration through a transverse slotted pipe. This reactor also uses mixing without damaging the filamentous bacteria. In this process, the mechanisms of bioremediation are identified.« less

Nanoporous aerogel as a bacteria repelling hygienic material for healthcare environment

NASA Astrophysics Data System (ADS)

Oh, Jun Kyun; Kohli, Nandita; Zhang, Yuanzhong; Min, Younjin; Jayaraman, Arul; Cisneros-Zevallos, Luis; Akbulut, Mustafa

2016-02-01

Healthcare-associated infections (HAIs) caused by pathogenic bacteria are a worldwide problem and responsible for numerous cases of morbidity and mortality. Exogenous cross-contamination is one of the main mechanisms contributing to such infections. This work investigates the potential of hydrophobically modified nanoporous silica aerogel as an antiadhesive hygienic material that can inhibit exogenous bacterial contamination. Nanoporous silica aerogels were synthesized via sol-gel polymerization of tetraethyl orthosilicate and hydrophobized using trimethylsilyl chloride. Bacterial adhesion characteristics were evaluated via dip-inoculation in suspensions of Gram-negative Escherichia coli O157:H7 and Gram-positive Staphylococcus aureus. The attachment of E. coli O157:H7 and S. aureus to hydrophobic nanoporous silica aerogel (HNSA) was found to be significantly lower than that to hydrophilic and hydrophobic nonporous silica materials: 99.91% (E. coli O157:H7) and 99.93% (S. aureus) reduction in comparison to hydrophilic nonporous silica, and 82.95% (E. coli O157:H7) and 84.90% (S. aureus) reduction in comparison to hydrophobic nonporous silica. These results suggest that the use of HNSA as surfaces that come into contact with bacterial pathogens in the healthcare environment can improve bacterial hygiene, and therefore may reduce the rate of HAIs.

Nanoporous aerogel as a bacteria repelling hygienic material for healthcare environment.

PubMed

Oh, Jun Kyun; Kohli, Nandita; Zhang, Yuanzhong; Min, Younjin; Jayaraman, Arul; Cisneros-Zevallos, Luis; Akbulut, Mustafa

2016-02-26

Healthcare-associated infections (HAIs) caused by pathogenic bacteria are a worldwide problem and responsible for numerous cases of morbidity and mortality. Exogenous cross-contamination is one of the main mechanisms contributing to such infections. This work investigates the potential of hydrophobically modified nanoporous silica aerogel as an antiadhesive hygienic material that can inhibit exogenous bacterial contamination. Nanoporous silica aerogels were synthesized via sol-gel polymerization of tetraethyl orthosilicate and hydrophobized using trimethylsilyl chloride. Bacterial adhesion characteristics were evaluated via dip-inoculation in suspensions of Gram-negative Escherichia coli O157:H7 and Gram-positive Staphylococcus aureus. The attachment of E. coli O157:H7 and S. aureus to hydrophobic nanoporous silica aerogel (HNSA) was found to be significantly lower than that to hydrophilic and hydrophobic nonporous silica materials: 99.91% (E. coli O157:H7) and 99.93% (S. aureus) reduction in comparison to hydrophilic nonporous silica, and 82.95% (E. coli O157:H7) and 84.90% (S. aureus) reduction in comparison to hydrophobic nonporous silica. These results suggest that the use of HNSA as surfaces that come into contact with bacterial pathogens in the healthcare environment can improve bacterial hygiene, and therefore may reduce the rate of HAIs.

Nursing management of reflex anoxic seizures in children.

PubMed

Patel, Neal; Kerr-Liddell, Rowan; Challis, Louise; Paul, Siba Prosad

2017-04-13

Children who present with transient loss of consciousness (T-LOC) are often first seen in emergency departments (EDs). Reflex anoxic seizure (RAS), vasovagal syncope and prolonged respiratory apnoea are benign, syncopal events that can be generally managed by explanation and reassurance. RAS is a short, paroxysmal, self-reverting episode of asystole that is triggered by pain, fear or anxiety and is caused by increased vagal response. It is an important differential diagnosis in pre-school age children who present with T-LOC, but is often underdiagnosed and can sometimes be misdiagnosed as epilepsy. Nurses working in EDs are among the first healthcare professionals to see children in acute settings and should therefore be aware of RAS, the presenting features and management options. This article discusses the epidemiology, pathophysiology and management of RAS, includes an illustrative case study and discusses the role of ED nurses.

Quantification of Spore-forming Bacteria Carried by Dust Particles

NASA Technical Reports Server (NTRS)

Lin, Ying; Cholakian, Tanya; Gao, Wenming; Osman, Shariff; Barengoltz, Jack

2006-01-01

In order to establish a biological contamination transport model for predicting the cross contamination risk during spacecraft assembly and upon landing on Mars, it is important to understand the relationship between spore-forming bacteria and their carrier particles. We conducted air and surface sampling in indoor, outdoor, and cleanroom environments to determine the ratio of spore forming bacteria to their dust particle carriers of different sizes. The number of spore forming bacteria was determined from various size groups of particles in a given environment. Our data also confirms the existence of multiple spores on a single particle and spore clumps. This study will help in developing a better bio-contamination transport model, which in turn will help in determining forward contamination risks for future missions.

Evidence For Volcanic Initiation Of Cretaceous Ocean Anoxic Events (Invited)

NASA Astrophysics Data System (ADS)

Sageman, B. B.; Hurtgen, M. T.; McElwain, J.; Adams, D.; Barclay, R. S.; Joo, Y.

2010-12-01

Increasing evidence from studies of Cretaceous ocean anoxic events (OAE’s) has suggested that major changes in volcanic activity may have played a significant role in their genesis. Numerous specific mechanisms of have been proposed, including increases in atmospheric CO2 and surface temperature, leading to enhanced chemical weathering and terrestrial nutrient release, or increases in reduced trace metal fluxes, leading to oxygen depletion and possibly providing micronutrients for enhanced primary production. An additional pathway by which the byproducts of enhanced volcanic activity may have contributed to OAE genesis involves relationships between the biogeochemical cycles sulfur, iron, and phosphorus. Recent analysis of S-isotope data from carbonate-associated sulfate and pyrite collected across the Cenomanian-Turonian OAE2 in the Western Interior basin suggest that increases in sulfate to an initially sulfate-depleted ocean preceded onset of the event. Modern lake data support the idea that increases in sulfate concentration drive microbial sulfate reduction, leading to more efficient regeneration of P from sedimentary organic matter. If the early Cretaceous opening of the South Atlantic was accompanied by evaporite deposition sufficient to draw down global marine sulfate levels, and widespread anoxia leading to elevated pyrite burial helped maintain these low levels for the succeeding 30 myr, during which most Cretaceous OAE’s are found, perhaps pulses of volcanism that rapidly introduced large volumes of sulfate may have played a key role in OAE initiation. The eventually burial of S in the form of pyrite may have returned sulfate levels to a low background, thus providing a mechanism to terminate the anoxic events. This talk will review the evidence for volcanic initiation of OAE’s in the context of the sulfate-phosphorus regeneration model.

Translational regulation in the anoxic turtle, Trachemys scripta elegans.

PubMed

Szereszewski, Kama E; Storey, Kenneth B

2017-12-14

The red-eared slider turtle (Trachemys scripta elegans), has developed remarkable adaptive mechanisms for coping with decreased oxygen availability during winter when lakes and ponds become covered with ice. Strategies for enduring anoxia tolerance include an increase in fermentable fuel reserves to support anaerobic glycolysis, the buffering of end products to minimize acidosis, altered expression in crucial survival genes, and strong metabolic rate suppression to minimize ATP-expensive metabolic processes such as protein synthesis. The mammalian target of rapamycin (mTOR) is at the center of the insulin-signaling pathway that regulates protein translation. The present study analyzed the responses of the mTOR signaling pathway to 5 (5H) or 20 h (20H) of anoxic submergence in liver and skeletal muscle of T. scripta elegans with a particular focus on regulatory changes in the phosphorylation states of targets. The data showed that phosphorylation of multiple mTOR targets was suppressed in skeletal muscle, but activated in the liver. Phosphorylated mTOR Ser2448 showed no change in skeletal muscle but had increased by approximately 4.5-fold in the liver after 20H of anoxia. The phosphorylation states of upstream positive regulators of mTOR (p-PDK-1 Ser241 , p-AKT Ser473 , and protein levels of GβL), the relative levels of dephosphorylated active PTEN, as well as phosphorylation state of negative regulators (TSC2 Thr1462 , p-PRAS40 Thr246 ) were generally found to be differentially regulated in skeletal muscle and in liver. Downstream targets of mTOR (p-p70 S6K Thr389 , p-S6 Ser235 , PABP, p-4E-BP1 Thr37/46 , and p-eIF4E Ser209 ) were generally unchanged in skeletal muscle but upregulated in most targets in liver. These findings indicate that protein synthesis is enhanced in the liver and suggests an increase in the synthesis of crucial proteins required for anoxic survival.

Fate of para-toluenesulfonamide (p-TSA) in groundwater under anoxic conditions: modelling results from a field site in Berlin (Germany).

PubMed

Meffe, Raffaella; Kohfahl, Claus; Hamann, Enrico; Greskowiak, Janek; Massmann, Gudrun; Dünnbier, Uwe; Pekdeger, Asaf

2014-01-01

This article reports on a field modelling study to investigate the processes controlling the plume evolution of para-toluenesulfonamide (p-TSA) in anoxic groundwater in Berlin, Germany. The organic contaminant p-TSA originates from the industrial production process of plasticisers, pesticides, antiseptics and drugs and is of general environmental concern for urban water management. Previous laboratory studies revealed that p-TSA is degradable under oxic conditions, whereas it appears to behave conservatively in the absence of oxygen (O2). p-TSA is ubiquitous in the aquatic environment of Berlin and present in high concentrations (up to 38 μg L(-1)) in an anoxic aquifer downgradient of a former sewage farm, where groundwater is partly used for drinking water production. To obtain refined knowledge of p-TSA transport and degradation in an aquifer at field scale, measurements of p-TSA were carried out at 11 locations (at different depths) between 2005 and 2010. Comparison of chloride (Cl(-)) and p-TSA field data showed that p-TSA has been retarded in the same manner as Cl(-). To verify the transport behaviour under field conditions, a two-dimensional transport model was setup, applying the dual-domain mass transfer approach in the model sector corresponding to an area of high aquifer heterogeneity. The distribution of Cl(-) and p-TSA concentrations from the site was reproduced well, confirming that both compounds behave conservatively and are subjected to retardation due to back diffusion from water stagnant zones. Predictive simulations showed that without any remediation measures, the groundwater quality near the drinking water well galleries will be affected by high p-TSA loads for about a hundred years.

Regulation of iron transport systems in Enterobacteriaceae in response to oxygen and iron availability.

PubMed

Carpenter, Chandra; Payne, Shelley M

2014-04-01

Iron is an essential nutrient for most bacteria. Depending on the oxygen available in the surrounding environment, iron is found in two distinct forms: ferrous (Fe(II)) or ferric (Fe(III)). Bacteria utilize different transport systems for the uptake of the two different forms of iron. In oxic growth conditions, iron is found in its insoluble, ferric form, and in anoxic growth conditions iron is found in its soluble, ferrous form. Enterobacteriaceae have adapted to transporting the two forms of iron by utilizing the global, oxygen-sensing regulators, ArcA and Fnr to regulate iron transport genes in response to oxygen. Copyright © 2014 Elsevier Inc. All rights reserved.

Comparative genomics of the lactic acid bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makarova, K.; Slesarev, A.; Wolf, Y.

Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive genemore » loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.« less

Abundance of genes involved in mercury methylation in oceanic environments

NASA Astrophysics Data System (ADS)

Palumbo, A. V.; Podar, M.; Gilmour, C. C.; Brandt, C. C.; Brown, S. D.; Crable, B. R.; Weighill, D.; Jacobson, D. A.; Somenahally, A. C.; Elias, D. A.

2016-02-01

The distribution and diversity of genes involved in mercury methylation in oceanic environments is of interest in determining the source of mercury in ocean environments and may have predictive value for mercury methylation rates. The highly conserved hgcAB genes involved in mercury methylation provide an avenue for evaluating the genetic potential for mercury methylation. The genes are sporadically present in a few diverse groups of bacteria and Archaea including Deltaproteobacteria, Firmicutes and Archaea and of over 7000 sequenced species they are only present in about 100 genomes. Examination of sequence data from methylators and non-methylators indicates that these genes are associated with other genes involved in metal transformations and transport. We examined hgcAB presence in over 3500 microbial metagenomes (from all environments) and found the hgcAB genes were present in anaerobic oceanic environments but not in aerobic layers of the open ocean. The genes were common in sediments from marine, coastal and estuarine sources as well as polluted environments. The genes were rare, found in 7 of 138 samples, in metagenomes from the pelagic water column including profiles though the oxygen minimum zone. Other oxic and sub-oxic coastal waters also demonstrated a lack of hgcAB genes including the OMZ in the Eastern North Pacific Ocean. There were some unique hgcA like unique sequences found in metagenomes from depth in the Pacific and Southern Atlantic Ocean. Coastal "dead zone" waters may be important sources of MeHg as the hgcAB genes were abundant in the anoxic waters of a stratified fjord. The genes were absent in microbiomes from vertebrates but were in invertebrate microbiomes However, oceanic species were underrepresented in these samples. Climate change could provide an additional flux of MeHg to the oceans as we found the most abundant representation of hgcAB genes in arctic permafrost. Thus warming could increase flux of methyl mercury to arctic waters.

Endophytic bacteria: prospects and applications for the phytoremediation of organic pollutants.

PubMed

Afzal, Muhammad; Khan, Qaiser M; Sessitsch, Angela

2014-12-01

Recently, there has been an increased effort to enhance the efficacy of phytoremediation of contaminated environments by exploiting plant-microbe interactions. The combined use of plants and endophytic bacteria is an emerging approach for the clean-up of soil and water polluted with organic compounds. In plant-endophyte partnerships, plants provide the habitat as well as nutrients to their associated endophytic bacteria. In response, endophytic bacteria with appropriate degradation pathways and metabolic activities enhance degradation of organic pollutants, and diminish phytotoxicity and evapotranspiration of organic pollutants. Moreover, endophytic bacteria possessing plant growth-promoting activities enhance the plant's adaptation and growth in soil and water contaminated with organic pollutants. Overall, the application of endophytic bacteria gives new insights into novel protocols to improve phytoremediation efficiency. However, successful application of plant-endophyte partnerships for the clean-up of an environment contaminated with organic compounds depends on the abundance and activity of the degrading endophyte in different plant compartments. Although many endophytic bacteria have the potential to degrade organic pollutants and improve plant growth, their contribution to enhance phytoremediation efficiency is still underestimated. A better knowledge of plant-endophyte interactions could be utilized to increase the remediation of polluted soil environments and to protect the foodstuff by decreasing agrochemical residues in food crops. Copyright © 2014 Elsevier Ltd. All rights reserved.

Arctic Ocean circulation during the anoxic Eocene Azolla event

NASA Astrophysics Data System (ADS)

Speelman, Eveline; Sinninghe Damsté, Jaap; März, Christian; Brumsack, Hans; Reichart, Gert-Jan

2010-05-01

The Azolla interval, as encountered in Eocene sediments from the Arctic Ocean, is characterized by organic rich sediments ( 4wt% Corg). In general, high levels of organic matter may be caused by increased productivity, i.e. extensive growth of Azolla, and/or enhanced preservation of organic matter, or a combination of both. Anoxic (bottom) water conditions, expanded oxygen minimum zones, or increased sedimentation rates all potentially increase organic matter preservation. According to plate tectonic, bathymetric, and paleogeographic reconstructions, the Arctic Ocean was a virtually isolated shallow basin, with one possible deeper connection to the Nordic Seas represented by a still shallow Fram Strait (Jakobsson et al., 2007), hampering ventilation of the Arctic Basin. During the Azolla interval surface waters freshened, while at the same time bottom waters appear to have remained saline, indicating that the Arctic was highly stratified. The restricted ventilation and stratification in concert with ongoing export of organic matter most likely resulted in the development of anoxic conditions in the lower part of the water column. Whereas the excess precipitation over evaporation maintained the freshwater lid, sustained input of Nordic Sea water is needed to keep the deeper waters saline. To which degree the Arctic Ocean exchanged with the Nordic Seas is, however, still largely unknown. Here we present a high-resolution trace metal record (ICP-MS and ICP-OES) for the expanded Early/Middle Eocene section capturing the Azolla interval from Integrated Ocean Drilling Program (IODP) Expedition 302 (ACEX) drilled on the Lomonosov Ridge, central Arctic Ocean. Euxinic conditions throughout the interval resulted in the efficient removal of redox sensitive trace metals from the water column. Using the sedimentary trace metal record we also constrained circulation in the Arctic Ocean by assessing the relative importance of trace metal input sources (i.e. fluvial, eolian, and

Nitrogen polishing in a fully anoxic anammox MBBR treating mainstream nitritation-denitritation effluent.

PubMed

Regmi, Pusker; Holgate, Becky; Miller, Mark W; Park, Hongkeun; Chandran, Kartik; Wett, Bernhard; Murthy, Sudhir; Bott, Charles B

2016-03-01

As nitrogen discharge limits are becoming more stringent, short-cut nitrogen systems and tertiary nitrogen polishing steps are gaining popularity. For partial nitritation or nitritation-denitritation systems, anaerobic ammonia oxidation (anammox) polishing may be feasible to remove residual ammonia and nitrite from the effluent. Nitrogen polishing of mainstream nitritation-denitritation system effluent via anammox was studied at 25°C in a fully anoxic moving bed bioreactor (MBBR) (V = 0.45 m(3) ) over 385 days. Unlike other anammox based processes, a very fast startup of anammox MBBR was demonstrated, despite nitrite limited feeding conditions (influent nitrite = 0.7 ± 0.59 mgN/L, ammonia = 6.13 ± 2.86 mgN/L, nitrate = 3.41 ± 1.92 mgN/L). The nitrogen removal performance was very stable within a wide range of nitrogen inputs. Anammox bacteria (AMX) activity up to 1 gN/m(2) /d was observed which is comparable to other biofilm-based systems. It is generally believed that nitrate production limits nitrogen removal through AMX metabolism. However, in this study, anammox MBBR demonstrated ammonia, nitrite, and nitrate removal at limited chemical oxygen demand (COD) availability. AMX and heterotrophs contributed to 0.68 ± 0.17 and 0.32 ± 0.17 of TIN removal, respectively. It was speculated that nitrogen removal might be aided by denitratation which could be due to heterotrophs or the recently discovered ability for AMX to use short-chain fatty acids to reduce nitrate to nitrite. This study demonstrates the feasibility of anammox nitrogen polishing in an MBBR is possible for nitritation-denitration systems. © 2015 Wiley Periodicals, Inc.

Most hydrocarbonoclastic bacteria in the total environment are diazotrophic, which highlights their value in the bioremediation of hydrocarbon contaminants.

PubMed

Dashti, Narjes; Ali, Nedaa; Eliyas, Mohamed; Khanafer, Majida; Sorkhoh, Naser A; Radwan, Samir S

2015-01-01

Eighty-two out of the 100 hydrocarbonoclastic bacterial species that have been already isolated from oil-contaminated Kuwaiti sites, characterized by 16S rRNA nucleotide sequencing, and preserved in our private culture collection, grew successfully in a mineral medium free of any nitrogenous compounds with oil vapor as the sole carbon source. Fifteen out of these 82 species were selected for further study based on the predominance of most of the isolates in their specific sites. All of these species tested positive for nitrogenase using the acetylene reduction reaction. They belonged to the genera Agrobacterium, Sphingomonas, and Pseudomonas from oily desert soil and Nesiotobacter, Nitratireductor, Acinetobacter, Alcanivorax, Arthrobacter, Marinobacter, Pseudoalteromonas, Vibrio, Diatzia, Mycobacterium, and Microbacterium from the Arabian/Persian Gulf water body. A PCR-DGGE-based sequencing analysis of nifH genes revealed the common occurrence of the corresponding genes among all the strains tested. The tested species also grew well and consumed crude oil effectively in NaNO3 -containing medium with and without nitrogen gas in the top space. On the other hand, these bacteria only grew and consumed crude oil in the NaNO3 -free medium when the top space gas contained nitrogen. We concluded that most hydrocarbonoclastic bacteria are diazotrophic, which allows for their wide distribution in the total environment. Therefore, these bacteria are useful for the cost-effective, environmentally friendly bioremediation of hydrocarbon contaminants.

Isolation of mesotrione-degrading bacteria from aquatic environments in Brazil

USDA-ARS?s Scientific Manuscript database

Mesotrione is a benzoylcyclohexane-1,3-dione herbicide that inhibits 4-hydroxyphenyl pyruvate dioxygenase (HPPD) in target plants. Although it has been used since 2000, only a limited number of degrading microorganisms have been reported. Mesotrione-degrading bacteria were selected among strains iso...

Variation of Oxygenation Conditions on a Hydrocarbonoclastic Microbial Community Reveals Alcanivorax and Cycloclasticus Ecotypes

PubMed Central

Terrisse, Fanny; Cravo-Laureau, Cristiana; Noël, Cyril; Cagnon, Christine; Dumbrell, Alex J.; McGenity, Terry J.; Duran, Robert

2017-01-01

Deciphering the ecology of marine obligate hydrocarbonoclastic bacteria (MOHCB) is of crucial importance for understanding their success in occupying distinct niches in hydrocarbon-contaminated marine environments after oil spills. In marine coastal sediments, MOHCB are particularly subjected to extreme fluctuating conditions due to redox oscillations several times a day as a result of mechanical (tide, waves and currents) and biological (bioturbation) reworking of the sediment. The adaptation of MOHCB to the redox oscillations was investigated by an experimental ecology approach, subjecting a hydrocarbon-degrading microbial community to contrasting oxygenation regimes including permanent anoxic conditions, anoxic/oxic oscillations and permanent oxic conditions. The most ubiquitous MOHCB, Alcanivorax and Cycloclasticus, showed different behaviors, especially under anoxic/oxic oscillation conditions, which were more favorable for Alcanivorax than for Cycloclasticus. The micro-diversity of 16S rRNA gene transcripts from these genera revealed specific ecotypes for different oxygenation conditions and their dynamics. It is likely that such ecotypes allow the colonization of distinct ecological niches that may explain the success of Alcanivorax and Cycloclasticus in hydrocarbon-contaminated coastal sediments during oil-spills. PMID:28861063

Relationships between sucretolerance and salinotolerance in bacteria from hypersaline environments and their implications for the exploration of Mars and the icy worlds

NASA Astrophysics Data System (ADS)

Fredsgaard, Casper; Moore, Donald B.; Al Soudi, Amer F.; Crisler, James D.; Chen, Fei; Clark, Benton C.; Schneegurt, Mark A.

2017-04-01

The most extremely osmotolerant microbial isolates are fungi from high-sugar environments that tolerate the lowest water activity (0.61) for growth yet reported. Studies of osmotolerant bacteria have focused on halotolerance rather than sucretolerance (ability to grow in high sugar concentrations). A collection of salinotolerant (>=10% NaCl or >=50% MgSO4) bacterial isolates from the Great Salt Plains of Oklahoma and Hot Lake in Washington were screened for sucretolerance in medium supplemented with >=50% fructose, glucose or sucrose. Tolerances significantly differed between solutes, even though water activities for saline media (0.92 and 0.85 for 10 and 20% NaCl Salt Plains media, respectively) were comparable or lower than water activities for high-sugar media (0.93 and 0.90 for 50 and 70% sucrose artificial nectar media, respectively). These specific solute effects were differentially expressed among individual isolates. Extrapolating the results of earlier food science studies with yeasts at high sugar concentrations to bacteria in salty environments with low water activity should be done with caution. Furthermore, the discussion of habitable Special Regions on Mars and the icy worlds should reflect an understanding of specific solute effects.

Molecular analyses of the microbial community composition of an anoxic basin of a municipal wastewater treatment plant reveal a novel lineage of proteobacteria.

PubMed

Chouari, Rakia; Le Paslier, Denis; Daegelen, Patrick; Dauga, Catherine; Weissenbach, Jean; Sghir, Abdelghani

2010-08-01

A culture-independent molecular phylogenetic approach was used to study prokaryotic diversity in an anoxic activated sludge from a municipal wastewater treatment plant. Two 16S rRNA gene libraries were constructed using total genomic DNA and amplified by polymerase chain reaction using primers specific for archaeal or bacterial domains. Phylogenetic analysis of 132 and 249 almost full-length 16S rRNA genes for Archaea and Bacteria, respectively, was done using the ARB software package. Phylogenetic groups affiliated with the Archaea belong to Euryarchaeota (93.8% of the operational taxonomic units [OTUs]) and Crenarchaeota (6.2% of the OTUs). Within the bacterial library, 84.8% of the OTUs represent novel putative phylotypes never described before and affiliated with ten divisions. The Proteobacteria phylum is the most abundant and diversified phylogenetic group representing 60.4% of the OTUs, followed by Bacteroidetes (22.1%) and gram-positives (6.1%). Interestingly, we detected a novel Proteobacteria monophyletic group distinct from the five known subclasses, which we named New Lineage of Proteobacteria (NLP) lineage, and it is composed of eight clones representing 4.6% of the Proteobacteria. A new 16S rRNA-targeted hybridization probe was designed and fluorescent in situ hybridization analyses shows representatives of NLP as cocci-shaped microorganisms. The Chloroflexi, Acidobacterium, and Nitrospira phyla and TM7 candidate division are each represented by ≤3% of clone sequences. A comprehensive set of eight 16S and 23S rRNA-targeted oligonucleotide probes was used to quantify these major groups by dot blot hybridization within 12 samples. The Proteobacteria accounted for 82.5 ± 4.9%, representing the most abundant phyla. The Bacteroidetes and Planctomycetales groups accounted for 4.9 ± 1.3% and 4 ± 1.7%, respectively. Firmicutes and Actinobacteria together accounted for only 1.9 ± 0.5%. The set of probes covers 93.4 ± 14% of the total

Enrichments for phototrophic bacteria and characterization by morphology and pigment analysis

NASA Technical Reports Server (NTRS)

Brune, D.

1985-01-01

The purpose of this investigation was to examine several sulfide containing environments for the presence of phototrophic bacteria and to obtain enriched cultures of some of the bacteria present. The field sites were Alum Rock State Park, the Palo Alto salt marsh, the bay area salt ponds, and Big Soda Lake (near Fallon, Nevada). Bacteria from these sites were characterized by microscopic examination, measurement of in vitro absorption spectra, and analysis of carotenoid pigments. Field observations at one of the bay area salt ponds, in which the salt concentration was saturating (about 30 percent NaCl) and the sediments along the shore of the pond covered with a gypsum crust, revealed a layer of purple photosynthetic bacteria under a green layer in the gypsum crust. Samples of this gypsum crust were taken to the laboratory to measure light transmission through the crust and to try to identify the purple photosynthetic bacteria present in this extremely saline environment.

Metabolic primers for detection of (Per)chlorate-reducing bacteria in the environment and phylogenetic analysis of cld gene sequences.

PubMed

Bender, Kelly S; Rice, Melissa R; Fugate, William H; Coates, John D; Achenbach, Laurie A

2004-09-01

Natural attenuation of the environmental contaminant perchlorate is a cost-effective alternative to current removal methods. The success of natural perchlorate remediation is dependent on the presence and activity of dissimilatory (per)chlorate-reducing bacteria (DPRB) within a target site. To detect DPRB in the environment, two degenerate primer sets targeting the chlorite dismutase (cld) gene were developed and optimized. A nested PCR approach was used in conjunction with these primer sets to increase the sensitivity of the molecular detection method. Screening of environmental samples indicated that all products amplified by this method were cld gene sequences. These sequences were obtained from pristine sites as well as contaminated sites from which DPRB were isolated. More than one cld phylotype was also identified from some samples, indicating the presence of more than one DPRB strain at those sites. The use of these primer sets represents a direct and sensitive molecular method for the qualitative detection of (per)chlorate-reducing bacteria in the environment, thus offering another tool for monitoring natural attenuation. Sequences of cld genes isolated in the course of this project were also generated from various DPRB and provided the first opportunity for a phylogenetic treatment of this metabolic gene. Comparisons of the cld and 16S ribosomal DNA (rDNA) gene trees indicated that the cld gene does not track 16S rDNA phylogeny, further implicating the possible role of horizontal transfer in the evolution of (per)chlorate respiration.

Characterization of the microbial community in a lotic environment to assess the effect of pollution on nitrifying and potentially pathogenic bacteria.

PubMed

Medeiros, J D; Araújo, L X; da Silva, V L; Diniz, C G; Cesar, D E; Del'Duca, A; Coelho, C M

2014-08-01

This study aimed to investigate microbes involved in the nitrogen cycle and potentially pathogenic bacteria from urban and rural sites of the São Pedro stream. Water samples were collected from two sites. A seasonal survey of bacterial abundance was conducted. The dissolved nutrient content was analysed. PCR and FISH analysis were performed to identify and quantify microbes involved in the nitrogen cycle and potentially pathogenic bacteria. The seasonal survey revealed that the bacterial abundance was similar along the year on the rural area but varied on the urban site. Higher concentration of dissolved nutrients in the urban area indicated a eutrophic system. Considering the nitrifying microbes, the genus Nitrobacter was found, especially in the urban area, and may act as the principal bacteria in converting nitrite into nitrate at this site. The molecular markers napA, amoA, and nfrA were more accumulated at the urban site, justifying the higher content of nutrients metabolised by these enzymes. Finally, high intensity of amplicons from Enterococcus, Streptococcus, Bacteroides/Prevotella/Porphyromonas, Salmonella, S. aureus, P. aeruginosa and the diarrheagenic lineages of E. coli were observed at the urban site. These results indicate a change in the structure of the microbial community imposed by anthrophic actions. The incidence of pathogenic bacteria in aquatic environments is of particular importance to public health, emphasising the need for sewage treatment to minimise the environmental impacts associated with urbanisation.

Systematic Review: Impact of point sources on antibiotic-resistant bacteria in the natural environment.

PubMed

Bueno, I; Williams-Nguyen, J; Hwang, H; Sargeant, J M; Nault, A J; Singer, R S

2018-02-01

Point sources such as wastewater treatment plants and agricultural facilities may have a role in the dissemination of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARG). To analyse the evidence for increases in ARB in the natural environment associated with these point sources of ARB and ARG, we conducted a systematic review. We evaluated 5,247 records retrieved through database searches, including both studies that ascertained ARG and ARB outcomes. All studies were subjected to a screening process to assess relevance to the question and methodology to address our review question. A risk of bias assessment was conducted upon the final pool of studies included in the review. This article summarizes the evidence only for those studies with ARB outcomes (n = 47). Thirty-five studies were at high (n = 11) or at unclear (n = 24) risk of bias in the estimation of source effects due to lack of information and/or failure to control for confounders. Statistical analysis was used in ten studies, of which one assessed the effect of multiple sources using modelling approaches; none reported effect measures. Most studies reported higher ARB prevalence or concentration downstream/near the source. However, this evidence was primarily descriptive and it could not be concluded that there is a clear impact of point sources on increases in ARB in the environment. To quantify increases in ARB in the environment due to specific point sources, there is a need for studies that stress study design, control of biases and analytical tools to provide effect measure estimates. © 2017 Blackwell Verlag GmbH.

[The value of glucose-positive coliform bacteria and potentially pathogenic bacteria as indicators of epidemiological safety of tap water].

PubMed

Zhuravlev, P V; Aleshnia, V V; Panasovets, O P; Morozova, A A; Artemova, T Z; Talaeva, Iu G; Zagaĭnova, A V; Gipp, E K

2012-01-01

Due to intensive anthropogenic pollution of water environment generally accepted indicators of epidemic security of water bodies - common bacteria and thermotolerant coliform bacteria do not always permit to obtain an objective characterization of bacterial contamination of tap water. From the point of view of authors the integral index - glucose positive coliform bacteria most adequately reflect the sanitary-hygienic and epidemiological situation of water bodies. In monitoring for bacterial quality of tap water it is advisable to determine glucose positive coliform bacteria, that will provide the relevance of estimation of the epidemiological safety of water use. According to the method developed by the authors the calculation of the index of population risk of acute intestinal infections occurrence in dependence on the quality of tap water in Azov and Tsimlyansk towns.

Identification and characterisation of isoprene-degrading bacteria in an estuarine environment.

PubMed

Johnston, Antonia; Crombie, Andrew T; El Khawand, Myriam; Sims, Leanne; Whited, Gregg M; McGenity, Terry J; Colin Murrell, J

2017-09-01

Approximately one-third of volatile organic compounds (VOCs) emitted to the atmosphere consists of isoprene, originating from the terrestrial and marine biosphere, with a profound effect on atmospheric chemistry. However, isoprene provides an abundant and largely unexplored source of carbon and energy for microbes. The potential for isoprene degradation in marine and estuarine samples from the Colne Estuary, UK, was investigated using DNA-Stable Isotope Probing (DNA-SIP). Analysis at two timepoints showed the development of communities dominated by Actinobacteria including members of the genera Mycobacterium, Rhodococcus, Microbacterium and Gordonia. Representative isolates, capable of growth on isoprene as sole carbon and energy source, were obtained from marine and estuarine locations, and isoprene-degrading strains of Gordonia and Mycobacterium were characterised physiologically and their genomes were sequenced. Genes predicted to be required for isoprene metabolism, including four-component isoprene monooxygenases (IsoMO), were identified and compared with previously characterised examples. Transcriptional and activity assays of strains growing on isoprene or alternative carbon sources showed that growth on isoprene is an inducible trait requiring a specific IsoMO. This study is the first to identify active isoprene degraders in estuarine and marine environments using DNA-SIP and to characterise marine isoprene-degrading bacteria at the physiological and molecular level. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Effects of ecological engineered oxygenation on the bacterial community structure in an anoxic fjord in western Sweden

PubMed Central

Forth, Michael; Liljebladh, Bengt; Stigebrandt, Anders; Hall, Per O J; Treusch, Alexander H

2015-01-01

Oxygen-depleted bodies of water are becoming increasingly common in marine ecosystems. Solutions to reverse this trend are needed and under development, for example, by the Baltic deep-water OXygenation (BOX) project. In the framework of this project, the Swedish Byfjord was chosen for a pilot study, investigating the effects of an engineered oxygenation on long-term anoxic bottom waters. The strong stratification of the water column of the Byfjord was broken up by pumping surface water into the deeper layers, triggering several inflows of oxygen-rich water and increasing oxygen levels in the lower water column and the benthic zone up to 110 μmol l−1.We used molecular ecologic methods to study changes in bacterial community structure in response to the oxygenation in the Byfjord. Water column samples from before, during and after the oxygenation as well as from two nearby control fjords were analyzed. Our results showed a strong shift in bacterial community composition when the bottom water in the Byfjord became oxic. Initially dominant indicator species for oxygen minimum zones such as members of the SUP05 clade declined in abundance during the oxygenation event and nearly vanished after the oxygenation was accomplished. In contrast, aerobic species like SAR11 that initially were restricted to surface waters could later be detected deep into the water column. Overall, the bacterial community in the formerly anoxic bottom waters changed to a community structure similar to those found in oxic waters, showing that an engineered oxygenation of a large body of anoxic marine water is possible and emulates that of a natural oxygenation event. PMID:25238400

Effects of ecological engineered oxygenation on the bacterial community structure in an anoxic fjord in western Sweden.

PubMed

Forth, Michael; Liljebladh, Bengt; Stigebrandt, Anders; Hall, Per O J; Treusch, Alexander H

2015-03-01

Oxygen-depleted bodies of water are becoming increasingly common in marine ecosystems. Solutions to reverse this trend are needed and under development, for example, by the Baltic deep-water OXygenation (BOX) project. In the framework of this project, the Swedish Byfjord was chosen for a pilot study, investigating the effects of an engineered oxygenation on long-term anoxic bottom waters. The strong stratification of the water column of the Byfjord was broken up by pumping surface water into the deeper layers, triggering several inflows of oxygen-rich water and increasing oxygen levels in the lower water column and the benthic zone up to 110 μmol l(-1).We used molecular ecologic methods to study changes in bacterial community structure in response to the oxygenation in the Byfjord. Water column samples from before, during and after the oxygenation as well as from two nearby control fjords were analyzed. Our results showed a strong shift in bacterial community composition when the bottom water in the Byfjord became oxic. Initially dominant indicator species for oxygen minimum zones such as members of the SUP05 clade declined in abundance during the oxygenation event and nearly vanished after the oxygenation was accomplished. In contrast, aerobic species like SAR11 that initially were restricted to surface waters could later be detected deep into the water column. Overall, the bacterial community in the formerly anoxic bottom waters changed to a community structure similar to those found in oxic waters, showing that an engineered oxygenation of a large body of anoxic marine water is possible and emulates that of a natural oxygenation event.

Interpreting the effect of increasing COD loading rates on the performance of a pre-anoxic MBBR system: implications on the attached and suspended biomass dynamics and nitrification-denitrification activity.

PubMed

Lima, P S; Dezotti, M; Bassin, J P

2016-06-01

A pre-anoxic MBBR system was subjected to increasing organic loading rates up to 18 gCOD/(m(2) day). At 3 gCOD/(m(2) day), most of the incoming organic matter was removed via denitrification. However, at higher loads, anoxic COD removal became limited by the nitrite/nitrate supply from the aerobic reactor, which assumed an important role in this conversion. Despite the application of low dissolved oxygen (DO) levels (<2 mg/L) in this tank, nitrification was observed to be nearly complete until 8 gCOD/(m(2) day). As the organic input was increased, the maximum specific nitrifying activity gradually declined. Activity tests suggested that an oxygen-limited environment was established in the biofilm. At lower loads [3-8 gCOD/(m(2) day)], the nitrification product obtained was affected by the DO concentration, whereas from 16 to 21 gCOD/(m(2) day), nitrite/nitrate profiles were likely associated with microbial stratification in the biofilm. The results also indicated that the role of the suspended biomass in the overall nitrification and denitrification can be very significant in high loaded MBBRs and should not be neglected, even at low HRTs.

Listeria monocytogenes strains show large variations in competitive growth in mixed culture biofilms and suspensions with bacteria from food processing environments.

PubMed

Heir, Even; Møretrø, Trond; Simensen, Andreas; Langsrud, Solveig

2018-06-20

Interactions and competition between resident bacteria in food processing environments could affect their ability to survive, grow and persist in microhabitats and niches in the food industry. In this study, the competitive ability of L. monocytogenes strains grown together in separate culture mixes with other L. monocytogenes (L. mono mix), L. innocua (Listeria mix), Gram-negative bacteria (Gram- mix) and with a multigenera mix (Listeria + Gram- mix) was investigated in biofilms on stainless steel and in suspensions at 12 °C. The mixed cultures included resident bacteria from processing surfaces in meat and salmon industry represented by L. monocytogenes (n = 6), L. innocua (n = 5) and Gram-negative bacteria (n = 6; Acinetobacter sp., Pseudomonas fragi, Pseudomonas fluorescens, Serratia liquefaciens, Stenotrophomonas maltophilia). Despite hampered in growth in mixed cultures, L. monocytogenes established in biofilms with counts at day nine between 7.3 and 9.0 log per coupon with the lowest counts in the Listeria + G- mix that was dominated by Pseudomonas. Specific L. innocua inhibited growth of L. monocytogenes strains differently; inhibition that was further enhanced by the background Gram-negative microbiota. In these multispecies and multibacteria cultures, the growth competitive effects lead to the dominance of a strong competitor L. monocytogenes strain that was only slightly inhibited by L. innocua and showed strong competitive abilities in mixed cultures with resident Gram-negative bacteria. The results indicates complex patterns of bacterial interactions and L. monocytogenes inhibition in the multibacteria cultures that only partially depend on cell contact and likely involve various antagonistic and bacterial tolerance mechanisms. The study indicates large variations among L. monocytogenes in their competitiveness under multibacterial culture conditions that should be considered in further studies towards understanding of L

Most Hydrocarbonoclastic Bacteria in the Total Environment are Diazotrophic, which Highlights Their Value in the Bioremediation of Hydrocarbon Contaminants

PubMed Central

Dashti, Narjes; Ali, Nedaa; Eliyas, Mohamed; Khanafer, Majida; Sorkhoh, Naser A.; Radwan, Samir S.

2015-01-01

Eighty-two out of the 100 hydrocarbonoclastic bacterial species that have been already isolated from oil-contaminated Kuwaiti sites, characterized by 16S rRNA nucleotide sequencing, and preserved in our private culture collection, grew successfully in a mineral medium free of any nitrogenous compounds with oil vapor as the sole carbon source. Fifteen out of these 82 species were selected for further study based on the predominance of most of the isolates in their specific sites. All of these species tested positive for nitrogenase using the acetylene reduction reaction. They belonged to the genera Agrobacterium, Sphingomonas, and Pseudomonas from oily desert soil and Nesiotobacter, Nitratireductor, Acinetobacter, Alcanivorax, Arthrobacter, Marinobacter, Pseudoalteromonas, Vibrio, Diatzia, Mycobacterium, and Microbacterium from the Arabian/Persian Gulf water body. A PCR-DGGE-based sequencing analysis of nifH genes revealed the common occurrence of the corresponding genes among all the strains tested. The tested species also grew well and consumed crude oil effectively in NaNO3 -containing medium with and without nitrogen gas in the top space. On the other hand, these bacteria only grew and consumed crude oil in the NaNO3 -free medium when the top space gas contained nitrogen. We concluded that most hydrocarbonoclastic bacteria are diazotrophic, which allows for their wide distribution in the total environment. Therefore, these bacteria are useful for the cost-effective, environmentally friendly bioremediation of hydrocarbon contaminants. PMID:25740314

Judo as a possible cause of anoxic brain damage. A case report.

PubMed

Owens, R G; Ghadiali, E J

1991-12-01

The rules of judo provide for strangulation techniques in which the blood supply to the brain is blocked by pressure on the carotid arteries; such techniques produce anoxia and possible unconsciousness if the victim fails to submit. A case is presented of a patient with signs of anoxic brain damage, with psychometric investigation showing memory disturbance consistent with a left temporal lobe lesion. This patient had been frequently strangled during his career as a judo player; it is suggested that such frequent strangulation was the cause of the damage. Such an observation indicates the need for caution in the use of such techniques.

Selection of bacteriocin producer strains of lactic acid bacteria from a dairy environment.

PubMed

Lasagno, M; Beoleito, V; Sesma, F; Raya, R; Font de Valdez, G; Eraso, A

2002-01-01

Two strains showing bacteriocin production were selected from a total of 206 lactic acid bacteria isolated from samples of milk, milk serum, whey and homemade cheeses in Southern Cordoba, Argentina. This property was detected by means of well diffusion assays. The strains were identified as Enterococcus hirae and Enterococcus durans. The protein nature of those substances was proved by showing their sensitivity to type IV and XXV proteases, papaine, trypsin, pepsin and K proteinase. The bacteriocins inhibited the growth of Listeria monocytogenes, Bacillus cereus, Clostridium perfringes and two strains of Staphylococcus aureus, an A-enterotoxin and a B-enterotoxin producers. All of these bacteria are common pathogens usually associated with food borne diseases (ETA). These lactic acid bacteria or their bacteriocins could be suitable candidates for food preservation and specially useful in the our regional dairy industry.

[The significance of glucose positive coliform bacteria and potentially pathogenic bacteria as an indicator of epidemiological safety of tap water].

PubMed

Zhuravlev, P V; Aleshnya, V V; Panasovets, O P; Morozova, A A; Artemova, T Z; Talaeva, Yu G; Zagaynova, A V

2013-01-01

Due to intensive anthropogenic pollution of water environment generally accepted indicators of epidemic security of water bodies--common bacteria (CB) and thermotolerant coliform bacteria (TCB) do not always permit to obtain an objective characterization of bacterial contamination of tap water. From the point of view of authors the integral index--glucose positive coliform bacteria most adequately reflect the sanitary-hygienic and epidemiological situation of water bodies. In monitoring for bacterial quality of tap water it is advisable to determine glucose positive coliform bacteria, that will provide the relevance of estimation of the epidemiological safety of water use. According to the method developed by the authors the calculation of the index of population risk of acute intestinal infections (AHI) occurrence in dependence on the quality of tap water in Azov and Tsimlyansk towns.

Are iron-phosphate minerals a sink for phosphorus in anoxic Black Sea sediments?

PubMed

Dijkstra, Nikki; Kraal, Peter; Kuypers, Marcel M M; Schnetger, Bernhard; Slomp, Caroline P

2014-01-01

Phosphorus (P) is a key nutrient for marine organisms. The only long-term removal pathway for P in the marine realm is burial in sediments. Iron (Fe) bound P accounts for a significant proportion of this burial at the global scale. In sediments underlying anoxic bottom waters, burial of Fe-bound P is generally assumed to be negligible because of reductive dissolution of Fe(III) (oxyhydr)oxides and release of the associated P. However, recent work suggests that Fe-bound P is an important burial phase in euxinic (i.e. anoxic and sulfidic) basin sediments in the Baltic Sea. In this study, we investigate the role of Fe-bound P as a potential sink for P in Black Sea sediments overlain by oxic and euxinic bottom waters. Sequential P extractions performed on sediments from six multicores along two shelf-to-basin transects provide evidence for the burial of Fe-bound P at all sites, including those in the euxinic deep basin. In the latter sediments, Fe-bound P accounts for more than 20% of the total sedimentary P pool. We suggest that this P is present in the form of reduced Fe-P minerals. We hypothesize that these minerals may be formed as inclusions in sulfur-disproportionating Deltaproteobacteria. Further research is required to elucidate the exact mineral form and formation mechanism of this P burial phase, as well as its role as a sink for P in sulfide-rich marine sediments.

[Respiratory protection provided by N95 filtering facepiece respirators and disposable medicine masks against airborne bacteria in different working environments].

PubMed

Lu, W; Zhu, X C; Zhang, X Y; Chen, Y T; Chen, W H

2016-09-20

Objective: To determine the relative protection provided by N95 filtering facepiece respirators (FFR) and disposable medicine masks (DMM) against airborne bacteria in different working environments. Methods: The field study was performed with 12 subjects wearing an N95 filtering facepiece respirator and a disposable medicine mask for 1h, respectively. Airborne microorganisms and bacteria samples from both the external (Ce) and the inner (Ci) surface of N95 FFR and DMM are collected. The Ce: Ci ratio was used to calculate the bacterial filtering proportion. Bacterial filtering efficiency (BFE) was measured using the JWL-2A Sampler. Results: The bacterial filtration efficiency of N95 FFR and DMM were 99.93% and 91.53%, respectively. There was significant difference between the two materials ( P <0.05). In summer, airborne bacterial concentration was higher than that in winter. In the same season, airborne bacterial concentration in hospital environment is higher than that in campus. The higher the airborne bacterial concentration, the greater bacterial contaminated on the external surface of the used masks. To all masks used in different working environment, bacterial contamination on the external surface was much greater than the inner surface ( P <0.01). Compared to N95 FFR, DMM had slighter bacterial contamination on the external surface and greater bacterial contamination on the inner surface. However, this difference was not significant ( P >0.05). The bacterial filtering proportion of N95 FFR is higher than DMM. These differences were significant in samples tested in summer ( P <0.05) , but were not significant in samples tested in winter ( P >0.05). Conclusion: Bacterial filtering efficiency of N95 respirator is superior to medicine mask, and this advantage become more obvious in high airborne bacterial concentration levels.

Psychrophilic and Psychrotolerant Microbial Extremophiles in Polar Environments

NASA Technical Reports Server (NTRS)

Hoover, Richard B.; Pikuta, Elena V.

2010-01-01

The microbial extremophiles that inhabit the polar regions of our planet are of tremendous significance. The psychrophilic and psychrotolerant microorganisms, which inhabit all of the cold environments on Earth have important applications to Bioremediation, Medicine, Pharmaceuticals, and many other areas of Biotechnology. Until recently, most of the research on polar microorganisms was confined to studies of polar diatoms, yeast, fungi and cyanobacteria. However, within the past three decades, extensive studies have been conducted to understand the bacteria and archaea that inhabit the Arctic and Antarctic sea-ice, glaciers, ice sheets, permafrost and the cryptoendolithic, cryoconite and ice-bubble environments. These investigations have resulted in the discovery of many new genera and species of anaerobic and aerobic microbial extremophiles. Exotic enzymes, cold-shock proteins and pigments produced by some of the extremophiles from polar environments have the potential to be of great benefit to Mankind. Knowledge about microbial life in the polar regions is crucial to understanding the limitations and biodiversity of life on Earth and may provide valuable clues to the Origin of Life on Earth. The discovery of viable microorganisms in ancient ice from the Fox Tunnel, Alaska and the deep Vostok Ice has shown that microorganisms can remain alive while cryopreserved in ancient ice. The psychrophilic lithoautotrophic homoacetogen isolated from the deep anoxic trough of Lake Untersee is an ideal candidate for life that might inhabit comets or the polar caps of Mars. The spontaneous release of gas from within the Anuchin Glacier above Lake Untersee may provide clues to the ice geysers that erupt from the tiger stripe regions of Saturn s moon Enceladus. The methane productivity in the lower regimes of Lake Untersee may also provide insights into possible mechanisms for the recently discovered methane releases on Mars. Since most of the other water bearing bodies of our

Nitrous oxide emission by aquatic macrofauna

PubMed Central

Stief, Peter; Poulsen, Morten; Nielsen, Lars Peter; Brix, Hans; Schramm, Andreas

2009-01-01

A large variety of aquatic animals was found to emit the potent greenhouse gas nitrous oxide when nitrate was present in the environment. The emission was ascribed to denitrification by ingested bacteria in the anoxic animal gut, and the exceptionally high N2O-to-N2 production ratio suggested delayed induction of the last step of denitrification. Filter- and deposit-feeding animal species showed the highest rates of nitrous oxide emission and predators the lowest, probably reflecting the different amounts of denitrifying bacteria in the diet. We estimate that nitrous oxide emission by aquatic animals is quantitatively important in nitrate-rich aquatic environments like freshwater, coastal marine, and deep-sea ecosystems. The contribution of this source to overall nitrous oxide emission from aquatic environments might further increase because of the projected increase of nitrate availability in tropical regions and the numeric dominance of filter- and deposit-feeders in eutrophic ecosystems. PMID:19255427

The Use of Bacteria for Remediation of Mercury Contaminated Groundwater

EPA Science Inventory

Many processes of mercury transformation in the environment are bacteria mediated. Mercury properties cause some difficulties of remediation of mercury contaminated environment. Despite the significance of the problem of mercury pollution, methods of large scale bioremediation ...

Decomposition of algal lipids in clay-enriched marine sediment under oxic and anoxic conditions

NASA Astrophysics Data System (ADS)

Lü, Dongwei; Song, Qian; Wang, Xuchen

2010-01-01

A series of laboratory incubation experiments were conducted to examine the decomposition of algal organic matter in clay-enriched marine sediment under oxic and anoxic conditions. During the 245-day incubation period, changes in the concentrations of TOC, major algal fatty acid components (14:0, 16:0, 16:1, 18:1 and 20:5), and n-alkanes (C16-C23) were quantified in the samples. Our results indicate that the organic matters were degraded more rapidly in oxic than anoxic conditions. Adsorption of fatty acids onto clay minerals was a rapid and reversible process. Using a simple G model, we calculated the decomposition rate constants for TOC, n-alkanes and fatty acids which ranged from 0.017-0.024 d-1, 0.049-0.103 d-1 and 0.011 to 0.069 d-1, respectively. Algal organic matter degraded in two stages characterized by a fast and a slow degradation processes. The addition of clay minerals montmorillonite and kaolinite to the sediments showed significant influence affecting the decomposition processes of algal TOC and fatty acids by adsorption and incorporation of the compounds with clay particles. Adsorption/association of fatty acids by clay minerals was rapid but appeared to be a slow reversible process. In addition to the sediment redox and clay influence, the structure of the compounds also played important roles in affecting their degradation dynamic in sediments.

Culturable diversity of halophilic bacteria in foreshore soils

PubMed Central

Irshad, Aarzoo; Ahmad, Irshad; Kim, Seung Bum

2014-01-01

Halophilic bacteria are commonly found in natural environments containing significant concentration of NaCl such as inland salt lakes and evaporated sea-shore pools, as well as environments such as curing brines, salted food products and saline soils. Dependence on salt is an important phenotypic characteristic of halophilic bacteria, which can be used in the polyphasic characterization of newly discovered microorganisms. In this study the diversity of halophilic bacteria in foreshore soils of Daecheon, Chungnam, and Saemangeum, Jeonbuk, was investigated. Two types of media, namely NA and R2A supplemented with 3%, 5%, 9%, 15%, 20% and 30% NaCl were used. More than 200 halophilic bacteria were isolated and BOX-PCR fingerprinting analysis was done for the typing of the isolates. The BLAST identification results showed that isolated strains were composed of 4 phyla, Firmicutes (60%), Proteobacteria (31%), Bacteriodetes (5%) and Actinobacteria (4%). Isolates were affiliated with 16 genera and 36 species. Bacillus was the dominant genus in the phylum Firmicutes, comprising 24% of the total isolates. Halomonas (12%) and Shewanella (12%) were also found as the main genera. These findings show that the foreshore soil of Daecheon Beach and Saemangeum Sea of Korea represents an untapped source of bacterial biodiversity. PMID:25242943

Culturable diversity of halophilic bacteria in foreshore soils.

PubMed

Irshad, Aarzoo; Ahmad, Irshad; Kim, Seung Bum

2014-01-01

Halophilic bacteria are commonly found in natural environments containing significant concentration of NaCl such as inland salt lakes and evaporated sea-shore pools, as well as environments such as curing brines, salted food products and saline soils. Dependence on salt is an important phenotypic characteristic of halophilic bacteria, which can be used in the polyphasic characterization of newly discovered microorganisms. In this study the diversity of halophilic bacteria in foreshore soils of Daecheon, Chungnam, and Saemangeum, Jeonbuk, was investigated. Two types of media, namely NA and R2A supplemented with 3%, 5%, 9%, 15%, 20% and 30% NaCl were used. More than 200 halophilic bacteria were isolated and BOX-PCR fingerprinting analysis was done for the typing of the isolates. The BLAST identification results showed that isolated strains were composed of 4 phyla, Firmicutes (60%), Proteobacteria (31%), Bacteriodetes (5%) and Actinobacteria (4%). Isolates were affiliated with 16 genera and 36 species. Bacillus was the dominant genus in the phylum Firmicutes, comprising 24% of the total isolates. Halomonas (12%) and Shewanella (12%) were also found as the main genera. These findings show that the foreshore soil of Daecheon Beach and Saemangeum Sea of Korea represents an untapped source of bacterial biodiversity.

Sphaerotilus natans encrusted with nanoball-shaped Fe(III) oxide minerals formed by nitrate-reducing mixotrophic Fe(II) oxidation

PubMed Central

Park, Sunhwa; Kim, Dong-Hun; Lee, Ji-Hoon; Hur, Hor-Gil

2014-01-01

Ferrous iron has been known to function as an electron source for iron-oxidizing microorganisms in both anoxic and oxic environments. A diversity of bacteria has been known to oxidize both soluble and solid-phase Fe(II) forms coupled to the reduction of nitrate. Here, we show for the first time Fe(II) oxidation by Sphaerotilus natans strain DSM 6575T under mixotrophic condition. Sphaerotilus natans has been known to form a sheath structure enclosing long chains of rod-shaped cells, resulting in a thick biofilm formation under oxic conditions. Here, we also demonstrate that strain DSM 6575T grows mixotrophically with pyruvate, Fe(II) as electron donors and nitrate as an electron acceptor and single cells of strain DSM 6575T are dominant under anoxic conditions. Furthermore, strain DSM 6575T forms nanoball-shaped amorphous Fe(III) oxide minerals encrusting on the cell surfaces through the mixotrophic iron oxidation reaction under anoxic conditions. We propose that cell encrustation results from the indirect Fe(II) oxidation by biogenic nitrite during nitrate reduction and that causes the bacterial morphological change to individual rod-shaped single cells from filamentous sheath structures. This study extends the group of existing microorganisms capable of mixotrophic Fe(II) oxidation by a new strain, S. natans strain DSM 6575T, and could contribute to biogeochemical cycles of Fe and N in the environment. PMID:24965827

Predictive isotopic biogeochemistry: hydrocarbons from anoxic marine basins

NASA Technical Reports Server (NTRS)

Freeman, K. H.; Wakeham, S. G.; Hayes, J. M.

1994-01-01

Carbon isotopic compositions were determined for individual hydrocarbons in water column and sediment samples from the Cariaco Trench and Black Sea. In order to identify hydrocarbons derived from phytoplankton, the isotopic compositions expected for biomass of autotrophic organisms living in surface waters of both localities were calculated based on the concentrations of CO2(aq) and the isotopic compositions of dissolved inorganic carbon. These calculated values are compared to measured delta values for particulate organic carbon and for individual hydrocarbon compounds. Specifically, we find that lycopane is probably derived from phytoplankton and that diploptene is derived from the lipids of chemoautotrophs living above the oxic/anoxic boundary. Three acyclic isoprenoids that have been considered markers for methanogens, pentamethyleicosane and two hydrogenated squalenes, have different delta values and apparently do not derive from a common source. Based on the concentration profiles and isotopic compositions, the C31 and C33 n-alkanes and n-alkenes have a similar source, and both may have a planktonic origin. If so, previously assigned terrestrial origins of organic matter in some Black Sea sediments may be erroneous.

Reduction of soybean meal non-starch polysaccharides and α-galactosides by solid-state fermentation using cellulolytic bacteria obtained from different environments.

PubMed

Opazo, Rafael; Ortúzar, Felipe; Navarrete, Paola; Espejo, Romilio; Romero, Jaime

2012-01-01

Soybean meal (SBM) is an important protein source in animal feed. However, the levels of SBM inclusion are restricted in some animal species by the presence of antinutritional factors (ANFs), including non-starch polysaccharides (NSPs) and α-galactosides (GOSs). The aim of this study was to reduce the soybean meal NSPs and GOSs by solid-state fermentation (SSF) using a combination of cellulolytic bacteria isolated from different environments (termites, earthworms, corn silage and bovine ruminal content). To analyse the key enzymatic activities, the isolates were grown in minimal media containing NSPs extracted from SBM. The selected bacterial strains belonged to the genera Streptomyces, Cohnella and Cellulosimicrobium. SSF resulted in a reduction of nearly 24% in the total NSPs, 83% of stachyose and 69% of raffinose and an increase in the protein content. These results suggest that cellulolytic bacteria-based SSF processing facilitates SBM nutritional improvement. In addition, the use of fermented SBM in animal diets can be recommended.

Versatile transformations of hydrocarbons in anaerobic bacteria: substrate ranges and regio- and stereo-chemistry of activation reactions†

PubMed Central

Jarling, René; Kühner, Simon; Basílio Janke, Eline; Gruner, Andrea; Drozdowska, Marta; Golding, Bernard T.; Rabus, Ralf; Wilkes, Heinz

2015-01-01

Anaerobic metabolism of hydrocarbons proceeds either via addition to fumarate or by hydroxylation in various microorganisms, e.g., sulfate-reducing or denitrifying bacteria, which are specialized in utilizing n-alkanes or alkylbenzenes as growth substrates. General pathways for carbon assimilation and energy gain have been elucidated for a limited number of possible substrates. In this work the metabolic activity of 11 bacterial strains during anaerobic growth with crude oil was investigated and compared with the metabolite patterns appearing during anaerobic growth with more than 40 different hydrocarbons supplied as binary mixtures. We show that the range of co-metabolically formed alkyl- and arylalkyl-succinates is much broader in n-alkane than in alkylbenzene utilizers. The structures and stereochemistry of these products are resolved. Furthermore, we demonstrate that anaerobic hydroxylation of alkylbenzenes does not only occur in denitrifiers but also in sulfate reducers. We propose that these processes play a role in detoxification under conditions of solvent stress. The thermophilic sulfate-reducing strain TD3 is shown to produce n-alkylsuccinates, which are suggested not to derive from terminal activation of n-alkanes, but rather to represent intermediates of a metabolic pathway short-cutting fumarate regeneration by reverse action of succinate synthase. The outcomes of this study provide a basis for geochemically tracing such processes in natural habitats and contribute to an improved understanding of microbial activity in hydrocarbon-rich anoxic environments. PMID:26441848

Nonproteinogenic D-amino acids at millimolar concentrations are a toxin for anaerobic microorganisms relevant to early Earth and other anoxic planets.

PubMed

Nixon, Sophie L; Cockell, Charles S

2015-03-01

The delivery of extraterrestrial organics to early Earth provided a potentially important source of carbon and energy for microbial life. Optically active organic compounds of extraterrestrial origin exist in racemic form, yet life on Earth has almost exclusively selected for L- over D-enantiomers of amino acids. Although D-enantiomers of proteinogenic amino acids are known to inhibit aerobic microorganisms, the role of concentrated nonproteinogenic meteoritic D-amino acids on anaerobic metabolisms relevant to early Earth and other anoxic planets such as Mars is unknown. Here, we test the inhibitory effect of D-enantiomers of two nonproteinogenic amino acids common to carbonaceous chondrites, norvaline and α-aminobutyric acid, on microbial iron reduction. Three pure strains (Geobacter bemidjiensis, Geobacter metallireducens, Geopsychrobacter electrodiphilus) and an iron-reducing enrichment culture were grown in the presence of 10 mM D-enantiomers of both amino acids. Further tests were conducted to assess the inhibitory effect of these D-amino acids at 1 and 0.1 mM. The presence of 10 mM D-norvaline and D-α-aminobutyric acid inhibited microbial iron reduction by all pure strains and the enrichment. G. bemidjiensis was not inhibited by either amino acid at 0.1 mM, but D-α-aminobutyric acid still inhibited at 1 mM. Calculations using published meteorite accumulation rates to the martian surface indicate D-α-aminobutyric acid may have reached inhibitory concentrations in little over 1000 years during peak infall. These data show that, on a young anoxic planet, the use of one enantiomer over another may render the nonbiological enantiomer an environmental toxin. Processes that generate racemic amino acids in the environment, such as meteoritic infall or impact synthesis, would have been toxic processes and could have been a selection pressure for the evolution of early racemases.

[Quorum sensing in bacteria and yeast].

PubMed

March Rosselló, Gabriel Alberto; Eiros Bouza, José María

2013-10-19

Bacterial sets are complex dynamic systems, which interact with each other and through the interaction, bacteria coexist, collaborate, compete and share information in a coordinated manner. A way of bacterial communication is quorum sensing. Through this mechanism the bacteria can recognize its concentration in a given environment and they can decide the time at which the expression of a particular set of genes should be started for developing a specific and simultaneous response. The result of these interconnections raises properties that cannot be explained from a single isolated bacterial cell. Copyright © 2012 Elsevier España, S.L. All rights reserved.

Communication among Oral Bacteria

PubMed Central

Kolenbrander, Paul E.; Andersen, Roxanna N.; Blehert, David S.; Egland, Paul G.; Foster, Jamie S.; Palmer, Robert J.

2002-01-01

Human oral bacteria interact with their environment by attaching to surfaces and establishing mixed-species communities. As each bacterial cell attaches, it forms a new surface to which other cells can adhere. Adherence and community development are spatiotemporal; such order requires communication. The discovery of soluble signals, such as autoinducer-2, that may be exchanged within multispecies communities to convey information between organisms has emerged as a new research direction. Direct-contact signals, such as adhesins and receptors, that elicit changes in gene expression after cell-cell contact and biofilm growth are also an active research area. Considering that the majority of oral bacteria are organized in dense three-dimensional biofilms on teeth, confocal microscopy and fluorescently labeled probes provide valuable approaches for investigating the architecture of these organized communities in situ. Oral biofilms are readily accessible to microbiologists and are excellent model systems for studies of microbial communication. One attractive model system is a saliva-coated flowcell with oral bacterial biofilms growing on saliva as the sole nutrient source; an intergeneric mutualism is discussed. Several oral bacterial species are amenable to genetic manipulation for molecular characterization of communication both among bacteria and between bacteria and the host. A successful search for genes critical for mixed-species community organization will be accomplished only when it is conducted with mixed-species communities. PMID:12209001

Transformation of heavy metal fractionation under changing environments: a case study of a drainage system in an e-waste dismantling community.

PubMed

Damrongsiri, Seelawut

2018-04-01

The change in environmental conditions during the transportation of contaminated soil and sediment was expected to affect the transformation of heavy metal fractionation. This study disclosed the serious contamination of copper (Cu), lead (Pb), and zinc (Zn) in the sewer sediment of an e-waste dismantling community in Thailand which may be caused by flushed contaminated soil and e-waste fragments. Two environmental conditions were simulated to observe the transformation of heavy metal fractionation. The anoxic sewer condition was induced using high substrate and sulfate in a closed container. The aeration of anoxic contaminated sediment was applied to simulate the transformation to an oxidative environment. The BCR sequential extraction was applied for heavy metal fractionation in this study. The study results exhibited that when heavy metal contaminated soil was transferred into this induced anoxic condition, fractionation was redistributed based on the chemical change of system that tends to be associated into F3 (oxidizable fraction) > F2 (reducible fraction) > F1 (acid soluble/exchangeable fraction). Cu exhibited the outstanding capability association to F3. The iron sulfide was not observed as usual due to its lower capability than Cu, Pb, and Zn. When contaminated sediment was transported to a more oxidative environment, the heavy metals fractionation would be redistributed again among those new environment media. It is noteworthy that F3 of Cu was stable even in oxic conditions. F2 of Fe was not developed by this oxic condition, possibly because its dehydration process was limited. The redistribution under an oxic environment became F1 > F2 > F3 indicating their more available form. This transformation was imperative and should be taken into account in heavy metal contaminated site management and control.

How Magnetotactic Bacteria Respond to Radiation Induced Stress and Damage: Comparative Genomics Evidences for Evolutionary Adaptation

NASA Astrophysics Data System (ADS)

Wang, Y.; Pan, Y.

2015-12-01

Solar radiation and galactic cosmic radiation is believed to be major restriction factors influencing survival and evolution of life. On planet earth, geomagnetic field along with atmosphere protect living beings from the harmful radiation. During a geomagnetic reversal or excursion, however, the efflux of charged particles on earth surface would increase as the shielding effect of magnetic field decrease. The stratospheric ozone can also be partially stripped away by solar wind when the strength of the field is weak, leading to an increasing ultraviolet radiation penetration to the earth surface. However, studies on the mechanism of radiation induced stress and damage are focused only on bacteria that have no response to magnetic field. This study was motivated by the need to fill the gap upon knowledge of that on magnetic field sensitive microorganism. Magnetotactic bacteria (MTB) are a group of microbes that are able to synthesis intracellular nano-sized magnetic particles (named magnetosomes). These chain-arranged magnetosomes help MTB sense and swim along the magnetic field to find their optimal living environment efficiently. In this paper, in silico prediction of stress and damage repair genes in response to different radiation were carried out on the complete genome of four nonmagnetotactic and four magnetotactic spirilla. In silico analyses of the genomes of magnetic field sensitive and non-sensitive spirilla revealed: 1) all strains contain genes for regulate responses superoxide and peroxide stress, DNA pyrimidine dimer and string breaks; 2) non-magnetotactic spirilla have more genes dealing with oxidative stress, while magnetotactic spirilla may benefit from magnetotaxis by swimming into oxic-anoxic zone away from oxidative stress and direct radiation damage; yet, the lipid hydroperoxide peroxidase gene in MTB may be responsible for possible ROS generated by the membrane enveloped magnetite magnetosome; 3) magnetotactic spirilla possess SOS rec

Cell surface characteristics enable encrustation-free survival of neutrophilic iron-oxidizing bacteria

NASA Astrophysics Data System (ADS)

Saini, G.; Chan, C. S.

2011-12-01

Microbial growth in mineralizing environments depends on the cells' ability to evade surface precipitation. Cell-mineral interactions may be required for metabolism, but if unmoderated, cells could become encrusted, which would limit diffusion of nutrients and waste across cell walls. A combination of cell surface charge and hydrophobicity could enable the survival of microbes in such environments by inhibiting mineral attachment. To investigate this mechanism, we characterized the surfaces of two neutrophilic iron-oxidizing bacteria (FeOB): Mariprofundus ferrooxydans, a Zetaproteobacterium from Fe(II)-rich submarine hydrothermal vents and a Betaproteobacterium Gallionellales strain R-1, recently isolated from a ferrous groundwater seep. Both bacteria produce iron oxyhydroxides, yet successfully escape surface encrustation while inhabiting milieu where iron minerals are also produced by abiotic processes. SEM-EDX and TEM-EELS analyses of cultured bacteria revealed no iron on the cell surfaces. Zeta potential measurements showed that these bacteria have very small negative surface charge (0 to -4 mV) over a pH range of 4-9, indicating near-neutrally charged surfaces. Water contact angle measurements and thermodynamic calculations demonstrate that both bacteria and abiotically-formed Fe oxhydroxides are hydrophilic. Extended-DLVO calculations showed that hydrophilic repulsion between cells and minerals dominates over electrostatic and Lifshitz-van der Waals interactions. This leads to overall repulsion between microbes and minerals, thus preventing surface encrustation. Low surface charge and hydrophilicity (determined by microbial adhesion to hydrocarbon assay) were common features for both live and azide-inhibited cells, which shows that surface characteristics do not depend on active metabolism. It is remarkable that these two phylogenetically-distant bacteria from different environments employ similar adaptations to prevent surface mineralization. Our results

Importance of the autumn overturn and anoxic conditions in the hypolimnion for the annual methane emissions from a temperate lake.

PubMed

Encinas Fernández, Jorge; Peeters, Frank; Hofmann, Hilmar

2014-07-01

Changes in the budget of dissolved methane measured in a small temperate lake over 1 year indicate that anoxic conditions in the hypolimnion and the autumn overturn period represent key factors for the overall annual methane emissions from lakes. During periods of stable stratification, large amounts of methane accumulate in anoxic deep waters. Approximately 46% of the stored methane was emitted during the autumn overturn, contributing ∼80% of the annual diffusive methane emissions to the atmosphere. After the overturn period, the entire water column was oxic, and only 1% of the original quantity of methane remained in the water column. Current estimates of global methane emissions assume that all of the stored methane is released, whereas several studies of individual lakes have suggested that a major fraction of the stored methane is oxidized during overturns. Our results provide evidence that not all of the stored methane is released to the atmosphere during the overturn period. However, the fraction of stored methane emitted to the atmosphere during overturn may be substantially larger and the fraction of stored methane oxidized may be smaller than in the previous studies suggesting high oxidation losses of methane. The development or change in the vertical extent and duration of the anoxic hypolimnion, which can represent the main source of annual methane emissions from small lakes, may be an important aspect to consider for impact assessments of climate warming on the methane emissions from lakes.

Diversity of protease-producing marine bacteria from sub-antarctic environments.

PubMed

Cristóbal, Héctor Antonio; López, Maria Alejandra; Kothe, Erika; Abate, Carlos Mauricio

2011-12-01

From seawater and the intestines of benthonic organisms collected from the Beagle Channel, Argentina, 230 marine bacteria were isolated. Cultivable bacteria were characterized and classified as psychrotolerant, whereas few isolates were psychrophiles. These isolates were capable of producing proteases at 4 and 15 °C under neutral (pH 7.0), alkaline (pH 10.0) and acidic (pH 4.5) conditions on different media, revealing 62, 33 and 22% producers at cold and 84, 47 and 33% producers at low temperatures, respectively. More protease-producing strains (67%) were detected when isolated from benthic invertebrates as compared to seawater (33%), with protease production under neutral conditions resulting in milk protein hydrolysis halos between 27 and 30 ± 2 mm in diameter. Using sterile 0.22 μm membrane filters, 29 isolates exhibiting extracellular protease activity were detected. These were grouped into six operational taxonomic units by restriction analysis and identified based on 16S rDNA as γ-proteobacteria of the genera Pseudoalteromonas, Pseudomonas, Shewanella, Alteromonas, Aeromonas, and Serratia. Plasmids were found to be harbored by eight strains, mainly within the isolates from benthonic organisms. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cadmium and zinc isotopes of organic-rich marine sediments during Oceanic Anoxic Event 2

NASA Astrophysics Data System (ADS)

Sweere, T.; Dickson, A. J.; Jenkyns, H. C.; Porcelli, D.; Henderson, G. M.; van den Boorn, S.

2017-12-01

Mesozoic Oceanic Anoxic Events (OAEs) are characterized by widespread deposition of organic-rich sediments and the spread of low-oxygen marine environments. To drive and sustain unusually efficient carbon-burial during these events requires high export productivity rates, which has to be supported by an abundance of nutrients in the surface ocean. The presence of redox-sensitive bio-essential micronutrients may be particularly important, and potentially bio-limiting, during such events as they may be drawn down into sediment under low-oxygen conditions. Cadmium and zinc isotopes have potential as tracers for past (micro)nutrient dynamics considering their nutrient-like distribution in the modern ocean and isotope fractionation with uptake by primary producers. The modern deep ocean is generally well mixed for Cd and Zn while short-term cycling of these elements in the surface ocean imposes regional variation. Additional regional variation may be caused by sulfide formation and associated isotope fractionation in euxinic environments. The impact of such regional environmental conditions on the Cd- and Zn-isotope composition of the sediment therefore needs to be addressed in order to explore the use of these elements as a proxy for past nutrient conditions. Here we present an extensive dataset of cadmium- and zinc-isotope compositions of organic-rich marine sediments from different basins deposited during OAE 2 (Late Cretaceous). This comparison highlights regional differences in Cd- and Zn-isotope compositions. However, despite regional environmental controls, a correlation between δ114Cd and δ66Zn across the different sites is observed, which implies a largely similar control on the two isotope systems. When regional environmental controls are accounted for, the data may provide insight in the δ66Zn and δ114Cd evolution of global seawater during OAE 2 as well as information on the global cycling of redox-sensitive micronutrients during the event

Seasonal Rates of Methane Oxidation in Anoxic Marine Sediments

PubMed Central

Iversen, Niels; Blackburn, T. Henry

1981-01-01

Methane concentrations and rates of methane oxidation were measured in intact sediment cores from an inshore marine sediment at Jutland, Denmark. The rates of methane oxidation, determined by the appearance of 14CO2 from injected 14CH4, varied with sediment depth and season. Most methane oxidation was anoxic, but oxygen may have contributed to methane oxidation at the sediment surface. Cumulative rates (0- to 12-cm depth) for methane oxidation at Kysing Fjord were 3.34, 3.48, 8.60, and 17.04 μmol m−2 day−1 for April (4°C), May (13°C), July (17°C), and August (21°C), respectively. If all of the methane was oxidized by sulfate, it would account for only 0.01 to 0.06% of the sulfate reduction. The data indicate that methane was produced, in addition to being oxidized, in the 0- to 18-cm sediment stratum. PMID:16345784

Evidence for Microbial Fe(III) Reduction in Anoxic, Mining-Impacted Lake Sediments (Lake Coeur d'Alene, Idaho)

PubMed Central

Cummings, David E.; March, Anthony W.; Bostick, Benjamin; Spring, Stefan; Caccavo, Frank; Fendorf, Scott; Rosenzweig, R. Frank

2000-01-01

Mining-impacted sediments of Lake Coeur d'Alene, Idaho, contain more than 10% metals on a dry weight basis, approximately 80% of which is iron. Since iron (hydr)oxides adsorb toxic, ore-associated elements, such as arsenic, iron (hydr)oxide reduction may in part control the mobility and bioavailability of these elements. Geochemical and microbiological data were collected to examine the ecological role of dissimilatory Fe(III)-reducing bacteria in this habitat. The concentration of mild-acid-extractable Fe(II) increased with sediment depth up to 50 g kg−1, suggesting that iron reduction has occurred recently. The maximum concentrations of dissolved Fe(II) in interstitial water (41 mg liter−1) occurred 10 to 15 cm beneath the sediment-water interface, suggesting that sulfidogenesis may not be the predominant terminal electron-accepting process in this environment and that dissolved Fe(II) arises from biological reductive dissolution of iron (hydr)oxides. The concentration of sedimentary magnetite (Fe3O4), a common product of bacterial Fe(III) hydroxide reduction, was as much as 15.5 g kg−1. Most-probable-number enrichment cultures revealed that the mean density of Fe(III)-reducing bacteria was 8.3 × 105 cells g (dry weight) of sediment−1. Two new strains of dissimilatory Fe(III)-reducing bacteria were isolated from surface sediments. Collectively, the results of this study support the hypothesis that dissimilatory reduction of iron has been and continues to be an important biogeochemical process in the environment examined. PMID:10618217

BioNLP Shared Task--The Bacteria Track.

PubMed

Bossy, Robert; Jourde, Julien; Manine, Alain-Pierre; Veber, Philippe; Alphonse, Erick; van de Guchte, Maarten; Bessières, Philippe; Nédellec, Claire

2012-06-26

We present the BioNLP 2011 Shared Task Bacteria Track, the first Information Extraction challenge entirely dedicated to bacteria. It includes three tasks that cover different levels of biological knowledge. The Bacteria Gene Renaming supporting task is aimed at extracting gene renaming and gene name synonymy in PubMed abstracts. The Bacteria Gene Interaction is a gene/protein interaction extraction task from individual sentences. The interactions have been categorized into ten different sub-types, thus giving a detailed account of genetic regulations at the molecular level. Finally, the Bacteria Biotopes task focuses on the localization and environment of bacteria mentioned in textbook articles. We describe the process of creation for the three corpora, including document acquisition and manual annotation, as well as the metrics used to evaluate the participants' submissions. Three teams submitted to the Bacteria Gene Renaming task; the best team achieved an F-score of 87%. For the Bacteria Gene Interaction task, the only participant's score had reached a global F-score of 77%, although the system efficiency varies significantly from one sub-type to another. Three teams submitted to the Bacteria Biotopes task with very different approaches; the best team achieved an F-score of 45%. However, the detailed study of the participating systems efficiency reveals the strengths and weaknesses of each participating system. The three tasks of the Bacteria Track offer participants a chance to address a wide range of issues in Information Extraction, including entity recognition, semantic typing and coreference resolution. We found common trends in the most efficient systems: the systematic use of syntactic dependencies and machine learning. Nevertheless, the originality of the Bacteria Biotopes task encouraged the use of interesting novel methods and techniques, such as term compositionality, scopes wider than the sentence.

Hydrogen generation by metal corrosion in simulated Waste Isolation Pilot Plant environments. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Telander, M.R.; Westerman, R.E.

1997-03-01

The corrosion and gas-generation characteristics of four material types: low-carbon steel (the current waste packaging material for the Waste Isolation Pilot Plant), Cu-base and Ti-base (alternative packaging) materials, and Al-base (simulated waste) materials were determined in both the liquid and vapor phase of Brine A, a brine representative of an intergranular Salado Formation brine. Test environments consisted primarily of anoxic brine with overpressures of N{sub 2}, CO{sub 2}, H{sub 2}S, and H{sub 2}. Limited tests of low-carbon steel were also performed in simulated-backfill environments and in brine environments with pH values ranging from 3 to 11. Low-carbon steel reacted atmore » a slow, measurable rate with anoxic brine, liberating H{sub 2} on an equimolar basis with Fe reacted. Presence of CO{sub 2} caused the initial reaction to proceed more rapidly, but CO{sub 2}-induced passivation stopped the reaction if the CO{sub 2} were present in sufficient quantities. Addition of H{sub 2}S to a CO{sub 2}-passivated system caused reversal of the passivation. Low-carbon steel immersed in brine with H{sub 2}S showed no reaction, apparently because of passivation of the steel by formation of FeS. Addition of CO{sub 2} to an H{sub 2}S-passivated system did not reverse the passivation. Cu- and Ti-base materials showed essentially no corrosion when exposed to brine and overpressures of N{sub 2}, CO{sub 2}, and H{sub 2}S except for the rapid and complete reaction between Cu-base materials and H{sub 2}S. The Al-base materials reacted at approximately the same rate as low-carbon steel when immersed in anoxic Brine A; considerably more rapidly in the presence of CO{sub 2} or H{sub 2}S; and much more rapidly when iron was present in the system as a brine contaminant. High-purity Al was much more susceptible to corrosion than the 6061 alloy. No significant reaction took place on any material in any environment in the vapor-phase exposures.« less

A simple method to model the reduced environment of lake bottom sapropel formation

NASA Astrophysics Data System (ADS)

Gaskova, Olga L.; Strakhovenko, Vera D.; Ermolaeva, Nadezhda I.; Zarubina, Eugene Yu.; Ovdina, Ekaterina A.

2017-07-01

The Kambala and Barchin brackish lakes (Baraba steppe, southern West Siberia) contain an organic-rich sapropel layer that was formed in oxygen-depleted waters. We measured the bulk sediment elemental composition, the water chemistry and determined the mineralogical composition and predominant biota species (Diatoms and Cyanobacteria in phytoplankton community respectively) in the lakes. The result indicates that the first lake has a siliceous type of sapropel and the second a carbonaceous one. A computer thermodynamic model was developed for chemical interaction in water-bottom sediment systems of the Kambala and Barchin Lakes. The surface sodium bicarbonate waters are supersaturated with respect to calcite, magnesite (or low Mg-calcite), quartz and chlorite with minor strontianite, apatite and goethite (pH 8.9-9.3, Eh 0.3 V). Nevertheless, it is shown that during sapropel deposition, deep silt waters should be anoxic (Eh<0 V). The virtual component CH2O has been used to create an anoxic environment suitable for pyrite formation due to the biotic community impact and abiotic reduction. Thermodynamic calculation has shown that silt water is not necessarily euxinic (anoxic and sulfidic). Depending on Eh, sulfate sulfur can dominate in solution, causing the formation of gypsum together with pyrite. An attempt was made to find a reason for solution supersaturation with respect to Ca and Mg ions due to their complexation with humic acids.

Anaerobic microbial communities in Lake Pavin, a unique meromictic lake in France.

PubMed

Lehours, Anne-C; Bardot, Corinne; Thenot, Aurelie; Debroas, Didier; Fonty, Gerard

2005-11-01

The Bacteria and Archaea from the meromictic Lake Pavin were analyzed in samples collected along a vertical profile in the anoxic monimolimnion and were compared to those in samples from the oxic mixolimnion. Nine targeted 16S rRNA oligonucleotide probes were used to assess the distribution of Bacteria and Archaea and to investigate the in situ occurrence of sulfate-reducing bacteria and methane-producing Archaea involved in the terminal steps of the anaerobic degradation of organic material. The diversity of the complex microbial communities was assessed from the 16S rRNA polymorphisms present in terminal restriction fragment (TRF) depth patterns. The densities of the microbial community increased in the anoxic layer, and Archaea detected with probe ARCH915 represented the largest microbial group in the water column, with a mean Archaea/Eubacteria ratio of 1.5. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed an elevated archaeal and bacterial phylotype richness in anoxic bottom-water samples. The structure of the Archaea community remained rather homogeneous, while TRFLP patterns for the eubacterial community revealed a heterogeneous distribution of eubacterial TRFs.

Identification of active fluorescence stained bacteria by Raman spectroscopy

NASA Astrophysics Data System (ADS)

Krause, Mario; Beyer, Beatrice; Pietsch, Christian; Radt, Benno; Harz, Michaela; Rösch, Petra; Popp, Jürgen

2008-04-01

Microorganisms can be found everywhere e.g. in food both as useful ingredients or harmful contaminations causing food spoilage. Therefore, a fast and easy to handle analysis method is needed to detect bacteria in different kinds of samples like meat, juice or air to decide if the sample is contaminated by harmful microorganisms. Conventional identification methods in microbiology require always cultivation and therefore are time consuming. In this contribution we present an analysis approach to identify fluorescence stained bacteria on strain level by means of Raman spectroscopy. The stained bacteria are highlighted and can be localized easier against a complex sample environment e.g. in food. The use of Raman spectroscopy in combination with chemometrical methods allows the identification of single bacteria within minutes.

Contribution of bacteria-like particles to PM2.5 aerosol in urban and rural environments

NASA Astrophysics Data System (ADS)

Wolf, R.; El-Haddad, I.; Slowik, J. G.; Dällenbach, K.; Bruns, E.; Vasilescu, J.; Baltensperger, U.; Prévôt, A. S. H.

2017-07-01

We report highly time-resolved estimates of airborne bacteria-like particle concentrations in ambient aerosol using an Aerodyne aerosol mass spectrometer (AMS). AMS measurements with a newly developed PM2.5 and the standard (PM1) aerodynamic lens were performed at an urban background site (Zurich) and at a rural site (Payerne) in Switzerland. Positive matrix factorization using the multilinear engine (ME-2) implementation was used to estimate the contribution of bacteria-like particles to non-refractory organic aerosol. The success of the method was evaluated by a size-resolved analysis of the organic mass and the analysis of single particle mass spectra, which were detected with a light scattering system integrated into the AMS. Use of the PM2.5 aerodynamic lens increased measured bacteria-like concentrations, supporting the analysis method. However, at all sites, the low concentrations of this component suggest that airborne bacteria constitute a minor fraction of non-refractory PM2.5 organic aerosol mass. Estimated average mass concentrations were below 0.1 μg/m3 and relative contributions were lower than 2% at both sites. During rainfall periods, concentrations of the bacteria-like component increased considerably reaching a short-time maximum of approximately 2 μg/m3 at the Payerne site in summer.

Human Occupancy as a Source of Indoor Airborne Bacteria

PubMed Central

Hospodsky, Denina; Qian, Jing; Nazaroff, William W.; Yamamoto, Naomichi; Bibby, Kyle; Rismani-Yazdi, Hamid; Peccia, Jordan

2012-01-01

Exposure to specific airborne bacteria indoors is linked to infectious and noninfectious adverse health outcomes. However, the sources and origins of bacteria suspended in indoor air are not well understood. This study presents evidence for elevated concentrations of indoor airborne bacteria due to human occupancy, and investigates the sources of these bacteria. Samples were collected in a university classroom while occupied and when vacant. The total particle mass concentration, bacterial genome concentration, and bacterial phylogenetic populations were characterized in indoor, outdoor, and ventilation duct supply air, as well as in the dust of ventilation system filters and in floor dust. Occupancy increased the total aerosol mass and bacterial genome concentration in indoor air PM10 and PM2.5 size fractions, with an increase of nearly two orders of magnitude in airborne bacterial genome concentration in PM10. On a per mass basis, floor dust was enriched in bacterial genomes compared to airborne particles. Quantitative comparisons between bacterial populations in indoor air and potential sources suggest that resuspended floor dust is an important contributor to bacterial aerosol populations during occupancy. Experiments that controlled for resuspension from the floor implies that direct human shedding may also significantly impact the concentration of indoor airborne particles. The high content of bacteria specific to the skin, nostrils, and hair of humans found in indoor air and in floor dust indicates that floors are an important reservoir of human-associated bacteria, and that the direct particle shedding of desquamated skin cells and their subsequent resuspension strongly influenced the airborne bacteria population structure in this human-occupied environment. Inhalation exposure to microbes shed by other current or previous human occupants may occur in communal indoor environments. PMID:22529946

Pathogen bacteria adhesion to skin mucus of fishes.

PubMed

Benhamed, Said; Guardiola, Francisco A; Mars, Mohammed; Esteban, María Ángeles

2014-06-25

Fish are always in intimate contact with their environment; therefore they are permanently exposed to very vary external hazards (e.g. aerobic and anaerobic bacteria, viruses, parasites, pollutants). To fight off pathogenic microorganisms, the epidermis and its secretion, the mucus acts as a barrier between the fish and the environment. Fish are surrounded by a continuous layer of mucus which is the first physical, chemical and biological barrier from infection and the first site of interaction between fish's skin cells and pathogens. The mucus composition is very complex and includes numerous antibacterial factors secreted by fish's skin cells, such as immunoglobulins, agglutinins, lectins, lysins and lysozymes. These factors have a very important role to discriminate between pathogenic and commensal microorganisms and to protect fish from invading pathogens. Furthermore, the skin mucus represents an important portal of entry of pathogens since it induces the development of biofilms, and represents a favorable microenvironment for bacteria, the main disease agents for fish. The purpose of this review is to summarize the current knowledge of the interaction between bacteria and fish skin mucus, the adhesion mechanisms of pathogens and the major factors influencing pathogen adhesion to mucus. The better knowledge of the interaction between fish and their environment could inspire other new perspectives to study as well as to exploit the mucus properties for different purposes. Copyright © 2014 Elsevier B.V. All rights reserved.

Effect of adaptation and pulp density on bioleaching of mine waste using indigenous acidophilic bacteria

NASA Astrophysics Data System (ADS)

Cho, K.; Kim, B.; Lee, D.; Choi, N.; Park, C.

2011-12-01

Adaptation to environment is a natural phenomena that takes place in many animals, plants and microorganisms. These adapted organisms achieve stronger applicability than unadapted organisms after habitation in a specific environment for a long time. In the biohydrometallurgical industry, adaptation to special environment conditions by selective culturing is the most popular method for improving bioleaching activity of strains-although that is time consuming. This study investigated the influence of the bioleaching efficiency of mine waste under batch experimental conditions (adaptation and pulp density) using the indigenous acidophilic bacteria collected from acid mine drainage in Go-seong and Yeon-hwa, Korea. We conducted the batch experiments at the influences of parameters, such as the adaptation of bacteria and pulp density of the mine waste. In the adaptation case, the value of pH in 1'st adaptation bacteria sample exhibited lower than in 2'nd adaptation bacteria sample. And the content of both Cu and Zn at 1'st adaptation bacteria sample appeared lower than at 2'nd adaptation bacteria sample. In the SEM analysis, the rod-shaped bacteria with 1μm in length were observed on the filter paper (pore size - 0.45μm). The results of pulp density experiments revealed that the content of both Cu and Zn increased with increasing pulp density, since the increment of pulp density resulted in the enhancement of bioleaching capacity.

Complete genome sequence of 'Halanaeroarchaeum sulfurireducens' M27-SA2, a sulfur-reducing and acetate-oxidizing haloarchaeon from the deep-sea hypersaline anoxic lake Medee.

PubMed

Messina, Enzo; Sorokin, Dimitry Y; Kublanov, Ilya V; Toshchakov, Stepan; Lopatina, Anna; Arcadi, Erika; Smedile, Francesco; La Spada, Gina; La Cono, Violetta; Yakimov, Michail M

2016-01-01

Strain M27-SA2 was isolated from the deep-sea salt-saturated anoxic lake Medee, which represents one of the most hostile extreme environments on our planet. On the basis of physiological studies and phylogenetic positioning this extremely halophilic euryarchaeon belongs to a novel genus 'Halanaeroarchaeum' within the family Halobacteriaceae. All members of this genus cultivated so far are strict anaerobes using acetate as the sole carbon and energy source and elemental sulfur as electron acceptor. Here we report the complete genome sequence of the strain M27-SA2 which is composed of a 2,129,244-bp chromosome and a 124,256-bp plasmid. This is the second complete genome sequence within the genus Halanaeroarchaeum. We demonstrate that genome of 'Halanaeroarchaeum sulfurireducens' M27-SA2 harbors complete metabolic pathways for acetate and sulfur catabolism and for de novo biosynthesis of 19 amino acids. The genomic analysis also reveals that 'Halanaeroarchaeum sulfurireducens' M27-SA2 harbors two prophage loci and one CRISPR locus, highly similar to that of Kulunda Steppe (Altai, Russia) isolate 'H. sulfurireducens' HSR2(T). The discovery of sulfur-respiring acetate-utilizing haloarchaeon in deep-sea hypersaline anoxic lakes has certain significance for understanding the biogeochemical functioning of these harsh ecosystems, which are incompatible with life for common organisms. Moreover, isolations of Halanaeroarchaeum members from geographically distant salt-saturated sites of different origin suggest a high degree of evolutionary success in their adaptation to this type of extreme biotopes around the world.

OPTIMIZATION OF VOLTAMMETRIC METHODS FOR AN IN SITU DETERMINATION OF TOTAL SULFIDE IN ANOXIC POREWATER USING A MERCURY PLATED GOLD ELECTRODE

EPA Science Inventory

Voltammetric methods for determination of total sulfide concentrations in anoxic sediments utilizing a previously described [1] gold-based mercury amalgam microelectrode were optimized. Systematic studies in NaCl (supporting electrolyte) and porewater indicate variations in ionic...

Multiresistant Bacteria Isolated from Chicken Meat in Austria

PubMed Central

Zarfel, Gernot; Galler, Herbert; Luxner, Josefa; Petternel, Christian; Reinthaler, Franz F.; Haas, Doris; Kittinger, Clemens; Grisold, Andrea J.; Pless, Peter; Feierl, Gebhard

2014-01-01

Multidrug resistant bacteria (MDR bacteria), such as extended spectrum beta-lactamase (ESBL) Enterobacteriaceae, methicillin resistant Staphylococcus aureus (MRSA), and vancomycin-resistant Enterococci (VRE), pose a challenge to the human health care system. In recent years, these MDR bacteria have been detected increasingly outside the hospital environment. Also the contamination of food with MDR bacteria, particularly of meat and meat products, is a concern. The aim of the study was to evaluate the occurrence of MDR bacteria in chicken meat on the Austrian market. For this study, 50 chicken meat samples were analysed. All samples originated from chickens slaughtered in Austrian slaughterhouses and were marked as produced in Austria. Samples were analysed for the presence of ESBL Enterobacteriaceae, methicillin resistant Staphylococci and VRE. Resistance genes of the isolated bacteria were characterised by PCR and sequencing. In the present study 26 ESBL producing E. coli, five mecA gene harbouring Staphylococci (but no MRSA), and four VRE were detected in chicken meat samples of Austrian origin. In 24 (48%) of the samples no ESBL Enterobacteriaceae, MRSA, methicillin resistant coagulase negative Staphylococcus (MRCNS) or VRE could be detected. None of the samples contained all three types of investigated multiresistant bacteria. In concordance to previous studies, CTX-M-1 and SHV-12 were the dominant ESBL genes. PMID:25485979

The Cenomanian-Turonian Oceanic Anoxic Event 2 (OAE2) in the Western Interior US and Gulf of Mexico: Decoupled Black Shale Deposition and Carbon Isotope Excursion

NASA Astrophysics Data System (ADS)

Lowery, C.; Snedden, J.; Cunningham, R.; Barrie, C.; Leckie, R. M.

2016-12-01

The largest carbon isotope excursions (CIEs) of the Cretaceous are associated with widespread evidence for marine anoxia and have been termed Oceanic Anoxic Events (OAEs). OAEs were originally thought to be globally-correlative intervals of black shales, but black shale deposition is an inherently provincial phenomenon driven by local conditions, and black shales associated with individual OAEs are often slightly diachronous and can be absent in some regions. Workers currently favor a definition of OAEs that is focused on the positive carbon isotope excursion driven by the global burial of organic matter and resulting carbon cycle perturbation; i.e., recording the global, rather than local, changes. While this is certainly the best way to define a global event, differences in the expression of the event between regions can be used to study the nature of the event itself. The greater Gulf of Mexico region in southern North America offers an excellent example of the diachroneity of black shale deposition and anoxia during one of the largest OAEs, the Cenomanian-Turonian OAE2. The Western Interior Seaway (WIS), flooded the interior of North America from the Gulf of Mexico up through the Canadian Arctic. In Texas and elsewhere across the WIS, high marine organic matter deposition and proxies for anoxia (especially benthic foraminifera and redox sensitive trace metals) are common before the event, but decrease at its onset, and in some places increase again after the event. Further south, across the Mexican shelf, deeper shelf environments remain dysoxic/anoxic through the event, while several carbonate platforms remain oxygenated during the event, but drown and record anoxic bottom waters shortly afterward. Here, we present new bulk carbonate and organic carbon isotopes and planktic and benthic foraminiferal populations from a 90 m core in southern Mississippi, USA, to present the first record of OAE2 from the northern Gulf of Mexico. In particular, we use

Cyclic diguanylate signaling in Gram-positive bacteria

PubMed Central

Purcell, Erin B.; Tamayo, Rita

2016-01-01

The nucleotide second messenger 3′-5′ cyclic diguanylate monophosphate (c-di-GMP) is a central regulator of the transition between motile and non-motile lifestyles in bacteria, favoring sessility. Most research investigating the functions of c-di-GMP has focused on Gram-negative species, especially pathogens. Recent work in Gram-positive species has revealed that c-di-GMP plays similar roles in Gram-positives, though the precise targets and mechanisms of regulation may differ. The majority of bacterial life exists in a surface-associated state, with motility allowing bacteria to disseminate and colonize new environments. c-di-GMP signaling regulates flagellum biosynthesis and production of adherence factors and appears to be a primary mechanism by which bacteria sense and respond to surfaces. Ultimately, c-di-GMP influences the ability of a bacterium to alter its transcriptional program, physiology and behavior upon surface contact. This review discusses how bacteria are able to sense a surface via flagella and type IV pili, and the role of c-di-GMP in regulating the response to surfaces, with emphasis on studies of Gram-positive bacteria. PMID:27354347

RNases and Helicases in Gram-Positive Bacteria.

PubMed

Durand, Sylvain; Condon, Ciaran

2018-04-01

RNases are key enzymes involved in RNA maturation and degradation. Although they play a crucial role in all domains of life, bacteria, archaea, and eukaryotes have evolved with their own sets of RNases and proteins modulating their activities. In bacteria, these enzymes allow modulation of gene expression to adapt to rapidly changing environments. Today, >20 RNases have been identified in both Escherichia coli and Bacillus subtilis , the paradigms of the Gram-negative and Gram-positive bacteria, respectively. However, only a handful of these enzymes are common to these two organisms and some of them are essential to only one. Moreover, although sets of RNases can be very similar in closely related bacteria such as the Firmicutes Staphylococcus aureus and B. subtilis , the relative importance of individual enzymes in posttranscriptional regulation in these organisms varies. In this review, we detail the role of the main RNases involved in RNA maturation and degradation in Gram-positive bacteria, with an emphasis on the roles of RNase J1, RNase III, and RNase Y. We also discuss how other proteins such as helicases can modulate the RNA-degradation activities of these enzymes.

Selection and Transmission of Antibiotic-Resistant Bacteria.

PubMed

Andersson, Dan I; Hughes, Diarmaid

2017-07-01

Ever since antibiotics were introduced into human and veterinary medicine to treat and prevent bacterial infections there has been a steady selection and increase in the frequency of antibiotic resistant bacteria. To be able to reduce the rate of resistance evolution, we need to understand how various biotic and abiotic factors interact to drive the complex processes of resistance emergence and transmission. We describe several of the fundamental factors that underlay resistance evolution, including rates and niches of emergence and persistence of resistant bacteria, time- and space-gradients of various selective agents, and rates and routes of transmission of resistant bacteria between humans, animals and other environments. Furthermore, we discuss the options available to reduce the rate of resistance evolution and/ or transmission and their advantages and disadvantages.

Evaluation of simultaneous nutrient and COD removal with polyhydroxybutyrate (PHB) accumulation using mixed microbial consortia under anoxic condition and their bioinformatics analysis.

PubMed

Jena, Jyotsnarani; Kumar, Ravindra; Dixit, Anshuman; Pandey, Sony; Das, Trupti

2015-01-01

Simultaneous nitrate-N, phosphate and COD removal was evaluated from synthetic waste water using mixed microbial consortia in an anoxic environment under various initial carbon load (ICL) in a batch scale reactor system. Within 6 hours of incubation, enriched DNPAOs (Denitrifying Polyphosphate Accumulating Microorganisms) were able to remove maximum COD (87%) at 2 g/L of ICL whereas maximum nitrate-N (97%) and phosphate (87%) removal along with PHB accumulation (49 mg/L) was achieved at 8 g/L of ICL. Exhaustion of nitrate-N, beyond 6 hours of incubation, had a detrimental effect on COD and phosphate removal rate. Fresh supply of nitrate-N to the reaction medium, beyond 6 hours, helped revive the removal rates of both COD and phosphate. Therefore, it was apparent that in spite of a high carbon load, maximum COD and nutrient removal can be maintained, with adequate nitrate-N availability. Denitrifying condition in the medium was evident from an increasing pH trend. PHB accumulation by the mixed culture was directly proportional to ICL; however the time taken for accumulation at higher ICL was more. Unlike conventional EBPR, PHB depletion did not support phosphate accumulation in this case. The unique aspect of all the batch studies were PHB accumulation was observed along with phosphate uptake and nitrate reduction under anoxic conditions. Bioinformatics analysis followed by pyrosequencing of the mixed culture DNA from the seed sludge revealed the dominance of denitrifying population, such as Corynebacterium, Rhodocyclus and Paraccocus (Alphaproteobacteria and Betaproteobacteria). Rarefaction curve indicated complete bacterial population and corresponding number of OTUs through sequence analysis. Chao1 and Shannon index (H') was used to study the diversity of sampling. "UCI95" and "LCI95" indicated 95% confidence level of upper and lower values of Chao1 for each distance. Values of Chao1 index supported the results of rarefaction curve.

Electron microscopic examination of uncultured soil-dwelling bacteria.

PubMed

Amako, Kazunobu; Takade, Akemi; Taniai, Hiroaki; Yoshida, Shin-ichi

2008-05-01

Bacteria living in soil collected from a rice paddy in Fukuoka, Japan, were examined by electron microscopy using a freeze-substitution fixation method. Most of the observed bacteria could be categorized, based on the structure of the cell envelope and overall morphology, into one of five groups: (i) bacterial spore; (ii) Gram-positive type; (iii) Gram-negative type; (iv) Mycobacterium like; and (v) Archaea like. However, a few of the bacteria could not be readily categorized into one of these groups because they had unique cell wall structures, basically resembling those of Gram-negative bacteria, but with the layer corresponding to the peptidoglycan layer in Gram-negative bacteria being extremely thick, like that of the cortex of a bacterial spore. The characteristic morphological features found in many of these uncultured, soil-dwelling cells were the nucleoid being in a condensed state and the cytoplasm being shrunken. We were able to produce similar morphologies in vitro using a Salmonella sp. by culturing under low-temperature, low-nutrient conditions, similar to those found in some natural environments. These unusual morphologies are therefore hypothesized to be characteristic of bacteria in resting or dormant stages.

Diverse algicidal bacteria associated with harmful bloom-forming Karenia mikimotoi in estuarine soil and seawater.

PubMed

Zheng, Ningning; Ding, Ning; Gao, Peike; Han, Meiaoxue; Liu, Xiuxia; Wang, Jianguo; Sun, Li; Fu, Baoyan; Wang, Renjun; Zhou, Jing

2018-08-01

Algicidal bacteria associated with Karenia mikimotoi have been isolated, yet the distribution of the algicidal bacteria has been rarely studied. Here, we postulated and demonstrated that terrestrial environment harbors diverse algicidal bacteria, which can survive in seawater along water flowing into marine and suppress Karenia mikimotoi. In summary, 9 and 5 bacteria with algicidal activity on Karenia mikimotoi were isolated from seawater and estuarine soil, respectively. Similar with the marine bacteria (Alteromonas sp., Halomonas sp., Marinobacter sp., Paracoccus sp., Rhodobacteraceae, Idiomarina sp.), the soil strains (Pseudoalteromonas sp. and Flavobaterium sp.) showed high mortality in Karenia mikimotoi with the inhibitory rate of 87% and 93.5%, respectively, after two days co-cultivation. Algicidal activity of the two strains was detected in the cell-free filtrate not in bacterial cells. The results suggest that algicidal bacteria associated with Karenia mikimotoi widely exist in terrestrial and marine environments, and have application potential on controlling Karenia mikimotoi. Copyright © 2018 Elsevier B.V. All rights reserved.

Buoyant densities of phototrophic sulfur bacteria and cyanobacteria

NASA Technical Reports Server (NTRS)

Guerrero, R.

1985-01-01

The buoyant densities of bacterial cells are greatly influenced by the accumulation of intracellular reserve material. The buoyant density of phototrophic bacteria that are planktonic is of particular interest, since these organisms must remain in the photic zone of the water column for optimal growth. Separation of cells by their buoyant density may also be of use in separating and identifying organisms from a natural population. The bacteria used were obtained from pure cultures, enrichments, or samples taken directly from the environment.

The study of a pilot-scale aerobic/Fenton/anoxic/aerobic process system for the treatment of landfill leachate.

PubMed

Hu, Wenyong; Zhou, Yu; Min, Xiaobo; Liu, Jingyi; Li, Xinyu; Luo, Lin; Zhang, Jiachao; Mao, Qiming; Chai, Liyuan; Zhou, YaoYu

2017-06-29

In this study, a combined aerobic-Fenton-anoxic/aerobic system was designed for the remediation of raw landfill leachate in a pilot-scale experiment. This system included (i) a granular sludge biological oxidation procedure that achieves the accumulation of nitrite nitrogen ([Formula: see text]) under aerobic conditions; (ii) a Fenton process that improves the biodegradability of the biotreated leachate and (iii) an activated sludge biological oxidation component under anoxic and aerobic conditions. Additionally, a shortcut nitrification and denitrification pathway was achieved. The effects of free ammonia, temperature and pH on nitrite accumulation were discussed. The change in the biochemical oxygen demand/chemical oxygen demand ratio of the effluent after shortcut nitrification was also analysed. The microbial community in the reactor were also investigated. The problem of the lack of carbon source in the denitrification process can be solved by the Fenton reagent method. Moreover, it was beneficial to achieving nitrogen removal as well as the more extensive removal of organic matter. The treatment strategy employed in this study exhibited good results and provided the potential practical application for treating landfill leachate.

Interactions between the microbiota and pathogenic bacteria in the gut

PubMed Central

Bäumler, Andreas J.; Sperandio, Vanessa

2016-01-01

The microbiome has an important role in human health. Changes in the microbiota can confer resistance to or promote infection by pathogenic bacteria. Antibiotics have a profound impact on the microbiota that alters the nutritional landscape of the gut and can lead to the expansion of pathogenic populations. Pathogenic bacteria exploit microbiota-derived sources of carbon and nitrogen as nutrients and regulatory signals to promote their own growth and virulence. By eliciting inflammation, these bacteria alter the intestinal environment and use unique systems for respiration and metal acquisition to drive their expansion. Unravelling the interactions between the microbiota, the host and pathogenic bacteria will produce strategies for manipulating the microbiota against infectious diseases. PMID:27383983

Interactions between the microbiota and pathogenic bacteria in the gut.

PubMed

Bäumler, Andreas J; Sperandio, Vanessa

2016-07-07

The microbiome has an important role in human health. Changes in the microbiota can confer resistance to or promote infection by pathogenic bacteria. Antibiotics have a profound impact on the microbiota that alters the nutritional landscape of the gut and can lead to the expansion of pathogenic populations. Pathogenic bacteria exploit microbiota-derived sources of carbon and nitrogen as nutrients and regulatory signals to promote their own growth and virulence. By eliciting inflammation, these bacteria alter the intestinal environment and use unique systems for respiration and metal acquisition to drive their expansion. Unravelling the interactions between the microbiota, the host and pathogenic bacteria will produce strategies for manipulating the microbiota against infectious diseases.

Indigenous soil bacteria and low moisture may limit but allow faecal bacteria to multiply and become a minor population in tropical soils

USGS Publications Warehouse

Byappanahalli, M.; Fujioka, R.

2004-01-01

The soil environment in Hawaii is generally characterised as sub-optimal but permissive to support the in situ growth of E. coli and enterococci. However, soil desiccation and competition for nutrients by major indigenous soil microflora have been identified as potential factors that could limit a rapid and continual growth of faecal indicator bacteria in this soil environment. Despite these limitations, the genetic capacities of E. coli and enterococci are robust enough to enable these bacteria to become established as minor populations of Hawaii's soil microflora. Although the concentrations of E. coli and enterococci may have represented a fraction of the total soil microbiota, their presence in this habitat was very significant, for two important reasons: (a) soil was a major environmental source of E. coli and enterococci, and (b) the elevated counts of these bacteria in streams that routinely exceeded the EPA standards were due to run-off from soil. As a result, E. coli and enterococci were inadequate indicators to measure the degree of faecal contamination and potential presence of sewage-borne pathogens in Hawaiian streams. ?? IWA Publishing 2004.

Fate and behavior of dissolved organic matter in a submerged anoxic-aerobic membrane bioreactor (MBR).

PubMed

Zhang, Dongqing; Trzcinski, Antoine Prandota; Luo, Jinxue; Stuckey, David C; Tan, Soon Keat

2018-02-01

In this study, the production, composition, and characteristics of dissolved organic matter (DOM) in an anoxic-aerobic submerged membrane bioreactor (MBR) were investigated. The average concentrations of proteins and carbohydrates in the MBR aerobic stage were 3.96 ± 0.28 and 8.36 ± 0.89 mg/L, respectively. After membrane filtration, these values decreased to 2.9 ± 0.2 and 2.8 ± 0.2 mg/L, respectively. High performance size exclusion chromatograph (HP-SEC) analysis indicated a bimodal molecular weight (MW) distribution of DOMs, and that the intensities of all the peaks were reduced in the MBR effluent compared to the influent. Three-dimensional fluorescence excitation emission matrix (FEEM) indicated that fulvic and humic acid-like substances were the predominant DOMs in biological treatment processes. Precise identification and characterization of low-MW DOMs was carried out using gas chromatography-mass spectrometry (GC-MS). The GC-MS analysis indicated that the highest peak numbers (170) were found in the anoxic stage, and 54 (32%) compounds were identified with a similarity greater than 80%. Alkanes (28), esters (11), and aromatics (7) were the main compounds detected. DOMs exhibited both biodegradable and recalcitrant characteristics. There were noticeable differences in the low-MW DOMs present down the treatment process train in terms of numbers, concentrations, molecular weight, biodegradability, and recalcitrance.

Communities of ammonia-oxidizing bacteria in activated sludge of various sewage treatment plants in Tokyo.

PubMed

Limpiyakorn, Tawan; Shinohara, Yuko; Kurisu, Futoshi; Yagi, Osami

2005-10-01

We investigated ammonia-oxidizing bacteria in activated sludge collected from 12 sewage treatment systems, whose ammonia removal and treatment processes differed, during three different seasons. We used real-time PCR quantification to reveal total bacterial numbers and total ammonia oxidizer numbers, and used specific PCR followed by denaturing gel gradient electrophoresis, cloning, and sequencing of 16S rRNA genes to analyze ammonia-oxidizing bacterial communities. Total bacterial numbers and total ammonia oxidizer numbers were in the range of 1.6 x 10(12) - 2.4 x 10(13) and 1.0 x 10(9) - 9.2 x 10(10)cellsl(-1), respectively. Seasonal variation was observed in the total ammonia oxidizer numbers, but not in the ammonia-oxidizing bacterial communities. Members of the Nitrosomonas oligotropha cluster were found in all samples, and most sequences within this cluster grouped within two of the four sequence types identified. Members of the clusters of Nitrosomonas europaea-Nitrosococcus mobilis, Nitrosomonas cryotolerans, and unknown Nitrosomonas, occurred solely in one anaerobic/anoxic/aerobic (A2O) system. Members of the Nitrosomonas communis cluster occurred almost exclusively in association with A2O and anaerobic/aerobic systems. Solid residence time mainly influenced the total numbers of ammonia-oxidizing bacteria, whereas dissolved oxygen concentration primarily affected the ammonia-oxidizing activity per ammonia oxidizer cell.

Tropical Archaea: Diversity associated with the surface microlayer of corals

USGS Publications Warehouse

Kellogg, C.A.

2004-01-01

Recent 16S rDNA studies have focused on detecting uncultivated bacteria associated with Caribbean reef corals in an effort to address the ecological roles of coral-associated microbes. Reports of Archaea associated with fishes and marine invertebrates raised the question of whether Archaea might also be part of the coral-associated microbial community. DNA analysis of mucus from 3 reef-building species of Caribbean corals, Montastraea annularis complex, Diploria strigosa and D. labyrinthiformis in the US Virgin Islands yielded 34 groups of archaeal 16S ribotypes (defined at the level of 97% similarity). The majority (75%) was most closely matched by BLAST searches to sequences derived from marine water column samples, whereas the remaining ribotypes were most similar to sequences isolated from anoxic environments (15%) and hydrothermal vents (9%). Unlike previous 16S studies of coral-associated Bacteria, the results do not suggest specific associations between particular archaeal sequences and individual coral species. Marine Archaea (Groups I, II and III) in addition to Thermoplasma-like, methanogen, and marine benthic crenarchaeote phylotypes, were detected in the mucus of tropical corals. The finding of sequences from coral-associated Archaea that are closely related to strict and facultative anaerobes, as well as to uncultivated Archaea from other types of anoxic environments, suggests that anaerobic micro-niches may exist in coral mucus layers. Archaea, with their unique biogeochemical capabilities, broaden the scope of possible interactions between corals and their associated microbial communities.

A comprehensive sulfur and oxygen isotope study of sulfur cycling in a shallow, hyper-euxinic meromictic lake

NASA Astrophysics Data System (ADS)

Gilhooly, William P.; Reinhard, Christopher T.; Lyons, Timothy W.

2016-09-01

Mahoney Lake is a permanently anoxic and sulfidic (euxinic) lake that has a dense plate of purple sulfur bacteria positioned at mid-water depth (∼7 m) where free sulfide intercepts the photic zone. We analyzed the isotopic composition of sulfate (δ34SSO4 and δ18OSO4), sulfide (δ34SH2S), and the water (δ18OH2O) to track the potentially coupled processes of dissimilatory sulfate reduction and phototrophic sulfide oxidation within an aquatic environment with extremely high sulfide concentrations (>30 mM). Large isotopic offsets observed between sulfate and sulfide within the monimolimnion (δ34SSO4-H2S = 51‰) and within pore waters along the oxic margin (δ34SSO4-H2S > 50‰) are consistent with sulfate reduction in both the sediments and the anoxic water column. Given the high sulfide concentrations of the lake, sulfur disproportionation is likely inoperable or limited to a very narrow zone in the chemocline, and therefore the large instantaneous fractionations are best explained by the microbial process of sulfate reduction. Pyrite extracted from the sediments reflects the isotopic composition of water column sulfide, suggesting that pyrite buried in the euxinic depocenter of the lake formed in the water column. The offset between sulfate and dissolved sulfide decreases at the chemocline (δ34SSO4-H2S = 37‰), a trend possibly explained by elevated sulfate reduction rates and inconsistent with appreciable disproportionation within this interval. Water column sulfate exhibits a linear response in δ18OSO4-δ34SSO4 and the slope of this relationship suggests relatively high sulfate reduction rates that appear to respond to seasonal changes in the productivity of purple sulfur bacteria. Although photosynthetic activity within the microbial plate influences the δ18OSO4-δ34SSO4 relationship, the biosignature for photosynthetic sulfur bacteria is restricted to the oxic/anoxic transition zone and is apparently minor relative to the more prevalent process of

Impact of simulated microgravity on the normal developmental time line of an animal-bacteria symbiosis

PubMed Central

Foster, Jamie S.; Khodadad, Christina L. M.; Ahrendt, Steven R.; Parrish, Mirina L.

2013-01-01

The microgravity environment during space flight imposes numerous adverse effects on animal and microbial physiology. It is unclear, however, how microgravity impacts those cellular interactions between mutualistic microbes and their hosts. Here, we used the symbiosis between the host squid Euprymna scolopes and its luminescent bacterium Vibrio fischeri as a model system. We examined the impact of simulated microgravity on the timeline of bacteria-induced development in the host light organ, the site of the symbiosis. To simulate the microgravity environment, host squid and symbiosis-competent bacteria were incubated together in high-aspect ratio rotating wall vessel bioreactors and examined throughout the early stages of the bacteria-induced morphogenesis. The host innate immune response was suppressed under simulated microgravity; however, there was an acceleration of bacteria-induced apoptosis and regression in the host tissues. These results suggest that the space flight environment may alter the cellular interactions between animal hosts and their natural healthy microbiome. PMID:23439280

Energetics of acclimation to NaCl by submerged, anoxic rice seedlings

PubMed Central

Kurniasih, Budiastuti; Greenway, Hank; Colmer, Timothy David

2017-01-01

Background and aims Our aim was to elucidate how plant tissues under a severe energy crisis cope with imposition of high NaCl, which greatly increases ion fluxes and hence energy demands. The energy requirements for ion regulation during combined salinity and anoxia were assessed to gain insights into ion transport processes in the anoxia-tolerant coleoptile of rice. Methods We studied the combined effects of anoxia plus 50 or 100 mm NaCl on tissue ions and growth of submerged rice (Oryza sativa) seedlings. Excised coleoptiles allowed measurements in aerated or anoxic conditions of ion net fluxes and O2 consumption or ethanol formation and by inference energy production. Key Results Over 80 h of anoxia, coleoptiles of submerged intact seedlings grew at 100 mm NaCl, but excised coleoptiles, with 50 mm exogenous glucose, survived only at 50 mm NaCl, possibly due to lower energy production with glucose than for intact coleoptiles with sucrose as substrate. Rates of net uptake of Na+ and Cl− by coleoptiles in anoxia were about half those in aerated solution. Ethanol formation in anoxia and O2 uptake in aerobic solution were each increased by 13–15 % at 50 mm NaCl, i.e. ATP formation was stimulated. For acclimation to 50 mm NaCl, the anoxic tissues used only 25 % of the energy that was expended by aerobic tissues. Following return of coleoptiles to aerated non-saline solution, rates of net K+ uptake recovered to those in continuously aerated solution, demonstrating there was little injury during anoxia with 50 mm NaCl. Conclusion Rice seedlings survive anoxia, without the coleoptile incurring significant injury, even with the additional energy demands imposed by NaCl (100 mm when intact, 50 mm when excised). Energy savings were achieved in saline anoxia by less coleoptile growth, reduced ion fluxes as compared to aerobic coleoptiles and apparent energy-economic ion transport systems. PMID:27694332

Importance of lactic acid bacteria in Asian fermented foods

PubMed Central

2011-01-01

Lactic acid bacteria play important roles in various fermented foods in Asia. Besides being the main component in kimchi and other fermented foods, they are used to preserve edible food materials through fermentation of other raw-materials such as rice wine/beer, rice cakes, and fish by producing organic acids to control putrefactive microorganisms and pathogens. These bacteria also provide a selective environment favoring fermentative microorganisms and produce desirable flavors in various fermented foods. This paper discusses the role of lactic acid bacteria in various non-dairy fermented food products in Asia and their nutritional and physiological functions in the Asian diet. PMID:21995342

Lactic Acid Bacteria Improves Peyer's Patch Cell-Mediated Immunoglobulin A and Tight-Junction Expression in a Destructed Gut Microbial Environment.

PubMed

Kim, Sung Hwan; Jeung, Woonhee; Choi, Il-Dong; Jeong, Ji-Woong; Lee, Dong Eun; Huh, Chul-Sung; Kim, Geun-Bae; Hong, Seong Soo; Shim, Jae-Jung; Lee, Jung Lyoul; Sim, Jae-Hun; Ahn, Young-Tae

2016-06-28

To evaluate the effects of lactic acid bacteria (LAB) on Peyer's patch cells, mice were treated with a high dose of kanamycin to disturb the gut microbial environment. The overarching goal was to explore the potential of LAB for use as a dietary probiotic that buffers the negative consequences of antibiotic treatment. In vitro, LAB stimulated the production of immunoglobulin A (IgA) from isolated Peyer's patch cells. Inflammation-related genes (TNF-α, IL-1β, and IL-8) were up-regulated in Caco-2 cells stimulated with lipopolysaccharide (LPS), while tight-junction-related genes (ZO-1 and occludin) were down-regulated; the effects of LPS on inflammatory gene and tight-junction gene expression were reversed by treatment with LAB. Mice treated with a high dose of kanamycin showed increased serum IgE levels and decreases in serum IgA and fecal IgA levels; the number of Peyer's patch cells decreased with kanamycin treatment. However, subsequent LAB treatment was effective in reducing the serum IgE level and recovering the serum IgA and fecal IgA levels, as well as the number of Peyer's patch cells. In addition, ZO-1 and occludin mRNA levels were up-regulated in the ileum tissues of mice receiving LAB treatment. Lactic acid bacteria can enhance the intestinal immune system by improving the integrity of the intestinal barrier and increasing the production of IgA in Peyer's patches. Lactic acid bacteria should be considered a potential probiotic candidate for improving intestinal immunity, particularly in mitigating the negative consequences of antibiotic use.

Methane production from bicarbonate and acetate in an anoxic marine sediment

NASA Technical Reports Server (NTRS)

Crill, P. M.; Martens, C. S.

1986-01-01

Methane production from C-14 labeled bicarbonate and acetate was measured over the top 28 cm of anoxic Cape Lookout Bight sediments during the summer of 1983. The depth distribution and magnitude of summed radioisotopically determined rates compare well with previous measurements of total methane production and the sediment-water methane flux. Methane production from CO2 reduction and acetate fermentation accounts for greater than 80 percent of the total production rate and sediment-water flux. Methane production from bicarbonate was found to occur in all depth intervals sampled except those in the top 2 cm, whereas significant methane production from acetate only occurred at depths below 10 cm where sulfate was exhausted. Acetate provided 20 to 29 percent of the measured methane production integrated over the top 30 cm of the sediments.

Isoprenoid quinones resolve the stratification of microbial redox processes in a biogeochemical continuum from the photic zone to deep anoxic sediments of the Black Sea.

PubMed

Becker, Kevin W; Elling, Felix J; Schröder, Jan M; Lipp, Julius S; Goldhammer, Tobias; Zabel, Matthias; Elvert, Marcus; Overmann, Jörg; Hinrichs, Kai-Uwe

2018-03-09

The stratified water column of the Black Sea serves as a model ecosystem for studying the interactions of microorganisms with major biogeochemical cycles. Here we provide detailed analysis of isoprenoid quinones to study microbial redox processes in the ocean. In a continuum from the photic zone through the chemocline into deep anoxic sediments of the southern Black Sea, diagnostic quinones and inorganic geochemical parameters indicate niche segregation between redox processes and corresponding shifts in microbial community composition. Quinones specific for oxygenic photosynthesis and aerobic respiration dominate oxic waters, while quinones associated with thaumarchaeal ammonia-oxidation and bacterial methanotrophy, respectively, dominate a narrow interval in suboxic waters. Quinone distributions indicate highest metabolic diversity within the anoxic zone, with anoxygenic photosynthesis being a major process in its photic layer. In the dark anoxic layer, quinone profiles indicate occurrence of bacterial sulfur and nitrogen cycling, archaeal methanogenesis, and archaeal methanotrophy. Multiple novel ubiquinone isomers, possibly originating from unidentified intra-aerobic anaerobes, occur in this zone. The respiration modes found in the anoxic zone continue into shallow subsurface sediments, but quinone abundances rapidly decrease within the upper 50 cm below sea floor, reflecting the transition to lower energy availability. In the deep subseafloor sediments, quinone distributions and geochemical profiles indicate archaeal methanogenesis/methanotrophy and potentially bacterial fermentative metabolisms. We observed that sedimentary quinone distributions track lithology, which supports prior hypotheses that deep biosphere community composition and metabolisms are determined by environmental conditions during sediment deposition. Importance Microorganisms play crucial roles in global biogeochemical cycles. Yet, we have only a fragmentary understanding of the diversity

INTERACTIONS OF INTRODUCED BACTERIA AND AQUATIC INVERTEBRATES

EPA Science Inventory

Bacteria enter into stream environments from a variety of sources and interact in varying ways with other biota. There were three basic objectives for this project: 1) to examine the effect of different types of macroinvertebrates on bacterial survival and distribution, 2) to com...

Characterization of airborne bacteria at an underground subway station.

PubMed

Dybwad, Marius; Granum, Per Einar; Bruheim, Per; Blatny, Janet Martha

2012-03-01

The reliable detection of airborne biological threat agents depends on several factors, including the performance criteria of the detector and its operational environment. One step in improving the detector's performance is to increase our knowledge of the biological aerosol background in potential operational environments. Subway stations are enclosed public environments, which may be regarded as potential targets for incidents involving biological threat agents. In this study, the airborne bacterial community at a subway station in Norway was characterized (concentration level, diversity, and virulence- and survival-associated properties). In addition, a SASS 3100 high-volume air sampler and a matrix-assisted laser desorption ionization-time of flight mass spectrometry-based isolate screening procedure was used for these studies. The daytime level of airborne bacteria at the station was higher than the nighttime and outdoor levels, and the relative bacterial spore number was higher in outdoor air than at the station. The bacterial content, particle concentration, and size distribution were stable within each environment throughout the study (May to September 2010). The majority of the airborne bacteria belonged to the genera Bacillus, Micrococcus, and Staphylococcus, but a total of 37 different genera were identified in the air. These results suggest that anthropogenic sources are major contributors to airborne bacteria at subway stations and that such airborne communities could harbor virulence- and survival-associated properties of potential relevance for biological detection and surveillance, as well as for public health. Our findings also contribute to the development of realistic testing and evaluation schemes for biological detection/surveillance systems by providing information that can be used to mimic real-life operational airborne environments in controlled aerosol test chambers.

Characterization of Airborne Bacteria at an Underground Subway Station

PubMed Central

Dybwad, Marius; Granum, Per Einar; Bruheim, Per

2012-01-01

The reliable detection of airborne biological threat agents depends on several factors, including the performance criteria of the detector and its operational environment. One step in improving the detector's performance is to increase our knowledge of the biological aerosol background in potential operational environments. Subway stations are enclosed public environments, which may be regarded as potential targets for incidents involving biological threat agents. In this study, the airborne bacterial community at a subway station in Norway was characterized (concentration level, diversity, and virulence- and survival-associated properties). In addition, a SASS 3100 high-volume air sampler and a matrix-assisted laser desorption ionization–time of flight mass spectrometry-based isolate screening procedure was used for these studies. The daytime level of airborne bacteria at the station was higher than the nighttime and outdoor levels, and the relative bacterial spore number was higher in outdoor air than at the station. The bacterial content, particle concentration, and size distribution were stable within each environment throughout the study (May to September 2010). The majority of the airborne bacteria belonged to the genera Bacillus, Micrococcus, and Staphylococcus, but a total of 37 different genera were identified in the air. These results suggest that anthropogenic sources are major contributors to airborne bacteria at subway stations and that such airborne communities could harbor virulence- and survival-associated properties of potential relevance for biological detection and surveillance, as well as for public health. Our findings also contribute to the development of realistic testing and evaluation schemes for biological detection/surveillance systems by providing information that can be used to mimic real-life operational airborne environments in controlled aerosol test chambers. PMID:22247150

Marine sulfate-reducing bacteria cause serious corrosion of iron under electroconductive biogenic mineral crust

PubMed Central

Enning, Dennis; Venzlaff, Hendrik; Garrelfs, Julia; Dinh, Hang T; Meyer, Volker; Mayrhofer, Karl; Hassel, Achim W; Stratmann, Martin; Widdel, Friedrich

2012-01-01

Iron (Fe0) corrosion in anoxic environments (e.g. inside pipelines), a process entailing considerable economic costs, is largely influenced by microorganisms, in particular sulfate-reducing bacteria (SRB). The process is characterized by formation of black crusts and metal pitting. The mechanism is usually explained by the corrosiveness of formed H2S, and scavenge of ‘cathodic’ H2 from chemical reaction of Fe0 with H2O. Here we studied peculiar marine SRB that grew lithotrophically with metallic iron as the only electron donor. They degraded up to 72% of iron coupons (10 mm × 10 mm × 1 mm) within five months, which is a technologically highly relevant corrosion rate (0.7 mm Fe0 year−1), while conventional H2-scavenging control strains were not corrosive. The black, hard mineral crust (FeS, FeCO3, Mg/CaCO3) deposited on the corroding metal exhibited electrical conductivity (50 S m−1). This was sufficient to explain the corrosion rate by electron flow from the metal (4Fe0 → 4Fe2+ + 8e−) through semiconductive sulfides to the crust-colonizing cells reducing sulfate (8e− + SO42− + 9H+ → HS− + 4H2O). Hence, anaerobic microbial iron corrosion obviously bypasses H2 rather than depends on it. SRB with such corrosive potential were revealed at naturally high numbers at a coastal marine sediment site. Iron coupons buried there were corroded and covered by the characteristic mineral crust. It is speculated that anaerobic biocorrosion is due to the promiscuous use of an ecophysiologically relevant catabolic trait for uptake of external electrons from abiotic or biotic sources in sediments. PMID:22616633

The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria.

PubMed

Ji, Boyang; Zhang, Sheng-Da; Zhang, Wei-Jia; Rouy, Zoe; Alberto, François; Santini, Claire-Lise; Mangenot, Sophie; Gagnot, Séverine; Philippe, Nadège; Pradel, Nathalie; Zhang, Lichen; Tempel, Sébastien; Li, Ying; Médigue, Claudine; Henrissat, Bernard; Coutinho, Pedro M; Barbe, Valérie; Talla, Emmanuel; Wu, Long-Fei

2017-03-01

Magnetotactic bacteria (MTB) are a group of phylogenetically and physiologically diverse Gram-negative bacteria that synthesize intracellular magnetic crystals named magnetosomes. MTB are affiliated with three classes of Proteobacteria phylum, Nitrospirae phylum, Omnitrophica phylum and probably with the candidate phylum Latescibacteria. The evolutionary origin and physiological diversity of MTB compared with other bacterial taxonomic groups remain to be illustrated. Here, we analysed the genome of the marine magneto-ovoid strain MO-1 and found that it is closely related to Magnetococcus marinus MC-1. Detailed analyses of the ribosomal proteins and whole proteomes of 390 genomes reveal that, among the Proteobacteria analysed, only MO-1 and MC-1 have coding sequences (CDSs) with a similarly high proportion of origins from Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria and Gammaproteobacteria. Interestingly, a comparative metabolic network analysis with anoxic network enzymes from sequenced MTB and non-MTB successfully allows the eventual prediction of an organism with a metabolic profile compatible for magnetosome production. Altogether, our genomic analysis reveals multiple origins of MO-1 and M. marinus MC-1 genomes and suggests a metabolism-restriction model for explaining whether a bacterium could become an MTB upon acquisition of magnetosome encoding genes. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics [Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics and NanoSIMS.

DOE PAGES

Burow, Luke C.; Woebken, Dagmar; Marshall, Ian PG; ...

2012-11-29

Photosynthetic microbial mats possess extraordinary phylogenetic and functional diversity that makes linking specific pathways with individual microbial populations a daunting task. Close metabolic and spatial relationships between Cyanobacteria and Chloroflexi have previously been observed in diverse microbial mats. Here in this paper, we report that an expressed metabolic pathway for the anoxic catabolism of photosynthate involving Cyanobacteria and Chloroflexi in microbial mats can be reconstructed through metatranscriptomic sequencing of mats collected at Elkhorn Slough, Monterey Bay, CA, USA. In this reconstruction, Microcoleus spp., the most abundant cyanobacterial group in the mats, ferment photosynthate to organic acids, CO 2 and Hmore » 2 through multiple pathways, and an uncultivated lineage of the Chloroflexi take up these organic acids to store carbon as polyhydroxyalkanoates. The metabolic reconstruction is consistent with metabolite measurements and single cell microbial imaging with fluorescence in situ hybridization and NanoSIMS.« less

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics [Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics and NanoSIMS.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burow, Luke C.; Woebken, Dagmar; Marshall, Ian PG

Photosynthetic microbial mats possess extraordinary phylogenetic and functional diversity that makes linking specific pathways with individual microbial populations a daunting task. Close metabolic and spatial relationships between Cyanobacteria and Chloroflexi have previously been observed in diverse microbial mats. Here in this paper, we report that an expressed metabolic pathway for the anoxic catabolism of photosynthate involving Cyanobacteria and Chloroflexi in microbial mats can be reconstructed through metatranscriptomic sequencing of mats collected at Elkhorn Slough, Monterey Bay, CA, USA. In this reconstruction, Microcoleus spp., the most abundant cyanobacterial group in the mats, ferment photosynthate to organic acids, CO 2 and Hmore » 2 through multiple pathways, and an uncultivated lineage of the Chloroflexi take up these organic acids to store carbon as polyhydroxyalkanoates. The metabolic reconstruction is consistent with metabolite measurements and single cell microbial imaging with fluorescence in situ hybridization and NanoSIMS.« less

Photogeochemical reactions of manganese under anoxic conditions

NASA Astrophysics Data System (ADS)

Liu, W.; Yee, N.; Piotrowiak, P.; Falkowski, P. G.

2017-12-01

Photogeochemistry describes reactions involving light and naturally occurring chemical species. These reactions often involve a photo-induced electron transfer that does not occur in the absence of light. Although photogeochemical reactions have been known for decades, they are often ignored in geochemical models. In particular, reactions caused by UV radiation during an ozone free early Earth could have influenced the available oxidation states of manganese. Manganese is one of the most abundant transition metals in the crust and is important in both biology and geology. For example, the presence of manganese (VI) oxides in the geologic record has been used as a proxy for oxygenic photosynthesis; however, we suggest that the high oxidation state of Mn can be produced abiotically by photochemical reactions. Aqueous solutions of manganese (II) as well as suspensions of rhodochrosite (MnCO3) were irradiated under anoxic condition using a 450 W mercury lamp and custom built quartz reaction vessels. The photoreaction of the homogeneous solution of Mn(II) produced H2 gas and akhtenskite (ɛ-MnO2) as the solid product . This product is different than the previously identified birnessite. The irradiation of rhodochrosite suspensions also produced H2 gas and resulted in both a spectral shift as well as morphology changes of the mineral particles in the SEM images. These reactions offer alternative, abiotic pathways for the formation of manganese oxides.

Control of microfabricated structures powered by flagellated bacteria using phototaxis

NASA Astrophysics Data System (ADS)

Steager, Edward; Kim, Chang-Beom; Patel, Jigarkumar; Bith, Socheth; Naik, Chandan; Reber, Lindsay; Kim, Min Jun

2007-06-01

Flagellated bacteria have been employed as microactuators in low Reynolds number fluidic environments. SU-8 microstructures have been fabricated and released on the surface of swarming Serratia marcescens, and the flagella propel the structures along the swarm surface. Phototactic control of these structures is demonstrated by exposing the localized regions of the swarm to ultraviolet light. The authors additionally discuss the control of microstructures in an open channel powered by bacteria which have been docked through a blotting technique. A tracking algorithm has been developed to analyze swarming patterns of the bacteria as well as the kinematics of the microstructures.

SULFATE-REDUCING BACTERIA IN THE SEAGRASS RHIZOSPHERE

EPA Science Inventory

Seagrasses are rooted in anoxic sediments that support high levels of microbial activity including utilization of sulfate as a terminal electron acceptor which is reduced to sulfide. Sulfate reduction in seagrass bed sediments is stimulated by input of organic carbon through the ...

Presence of bacteria in the endometrium and placentomes of pregnant cows.

PubMed

Karstrup, Cecilia Christensen; Klitgaard, Kirstine; Jensen, Tim Kåre; Agerholm, Jørgen Steen; Pedersen, Hanne Gervi

2017-09-01

Bacterial invasion of the bovine uterus during the postpartum period occurs in most cows, but the general consensus is that these bacteria are eliminated before the next pregnancy. The pregnant uterus has therefore hitherto been considered a sterile environment, but this assumption has now been challenged by recent studies in humans, which indicate that bacteria can be present in the placenta of term pregnancies without causing abortion. The aim of the present study was therefore to investigate whether bacteria are present in the uterus of pregnant cows. Specimens were taken from the inter-caruncular endometrium and from placentomes of slaughtered pregnant cows (n = 43) and subjected to histology, fluorescence in situ hybridization and massive parallel sequencing. Bacteria were observed in the tissue from 90.7% (39/43) of the cows by fluorescence in situ hybridization. Fusobacterium necrophorum, Porphyromonas levii and Trueperella pyogenes were located within the endometrium, on the endometrial surface and in the caruncular stroma, but their presence was not associated with inflammation. Data from massive parallel sequencing of the 16S rRNA gene from a subset of 15 cows indicated that the most abundant bacteria were the families Porphyromonadaceae, followed by Ruminococcaceae and Lachnospiraceae. Our results indicate that the bovine uterus is not a sterile environment during pregnancy as previously assumed and that a cow can carry a pregnancy despite the presence of a few potentially pathogenic bacteria in the uterus. Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular and chemical dialogues in bacteria-protozoa interactions.

PubMed

Song, Chunxu; Mazzola, Mark; Cheng, Xu; Oetjen, Janina; Alexandrov, Theodore; Dorrestein, Pieter; Watrous, Jeramie; van der Voort, Menno; Raaijmakers, Jos M

2015-08-06

Protozoan predation of bacteria can significantly affect soil microbial community composition and ecosystem functioning. Bacteria possess diverse defense strategies to resist or evade protozoan predation. For soil-dwelling Pseudomonas species, several secondary metabolites were proposed to provide protection against different protozoan genera. By combining whole-genome transcriptome analyses with (live) imaging mass spectrometry (IMS), we observed multiple changes in the molecular and chemical dialogues between Pseudomonas fluorescens and the protist Naegleria americana. Lipopeptide (LP) biosynthesis was induced in Pseudomonas upon protozoan grazing and LP accumulation transitioned from homogeneous distributions across bacterial colonies to site-specific accumulation at the bacteria-protist interface. Also putrescine biosynthesis was upregulated in P. fluorescens upon predation. We demonstrated that putrescine induces protozoan trophozoite encystment and adversely affects cyst viability. This multifaceted study provides new insights in common and strain-specific responses in bacteria-protozoa interactions, including responses that contribute to bacterial survival in highly competitive soil and rhizosphere environments.

Jellyfish Lake, Palau: early diagenesis of organic matter in sediments of an anoxic marine lake

USGS Publications Warehouse

Orem, W.H.; Burnett, W.C.; Landing, W.M.; Lyons, W.B.; Showers, W.

1991-01-01

The major postdepositional change in the sedimentary organic matter is carbohydrate biodegradation. Lignin and aliphatic substances are preserved in the sediments. Dissolved organic matter in pore waters is primarily composed of carbohydrates, reflecting the degradation of sedimentary carbohydrates. Rate constants for organic carbon degradation and sulfate reduction in sediments of the lake are about 10?? lower than in other anoxic sediments. This may reflect the vascular plant source and partly degraded nature of the organic matter reaching the sediments of the lake. -from Authors

Plutonium Oxidation State Distribution under Aerobic and Anaerobic Subsurface Conditions for Metal-Reducing Bacteria

NASA Astrophysics Data System (ADS)

Reed, D. T.; Swanson, J.; Khaing, H.; Deo, R.; Rittmann, B.

2009-12-01

The fate and potential mobility of plutonium in the subsurface is receiving increased attention as the DOE looks to cleanup the many legacy nuclear waste sites and associated subsurface contamination. Plutonium is the near-surface contaminant of concern at several DOE sites and continues to be the contaminant of concern for the permanent disposal of nuclear waste. The mobility of plutonium is highly dependent on its redox distribution at its contamination source and along its potential migration pathways. This redox distribution is often controlled, especially in the near-surface where organic/inorganic contaminants often coexist, by the direct and indirect effects of microbial activity. The redox distribution of plutonium in the presence of facultative metal reducing bacteria (specifically Shewanella and Geobacter species) was established in a concurrent experimental and modeling study under aerobic and anaerobic conditions. Pu(VI), although relatively soluble under oxidizing conditions at near-neutral pH, does not persist under a wide range of the oxic and anoxic conditions investigated in microbiologically active systems. Pu(V) complexes, which exhibit high chemical toxicity towards microorganisms, are relatively stable under oxic conditions but are reduced by metal reducing bacteria under anaerobic conditions. These facultative metal-reducing bacteria led to the rapid reduction of higher valent plutonium to form Pu(III/IV) species depending on nature of the starting plutonium species and chelating agents present in solution. Redox cycling of these lower oxidation states is likely a critical step in the formation of pseudo colloids that may lead to long-range subsurface transport. The CCBATCH biogeochemical model is used to explain the redox mechanisms and final speciation of the plutonium oxidation state distributions observed. These results for microbiologically active systems are interpreted in the context of their importance in defining the overall migration

Factors of bacteria and virus transport in groundwater

NASA Astrophysics Data System (ADS)

Pekdeger, A.; Matthess, G.

1983-06-01

The underground transport of pathogenic bacteria and viruses may be described by the general transport equation considering dispersion, adsorption, and biological elimination. The survival time of bacteria and viruses in groundwater is different for the specific species and for the specific groundwater environment. Dispersion causes a distribution of pollutants in time and space, thus their concentration decreases over time and with transport distance. Microorganisms are reversibly adsorbed on underground particles, which causes a retardation of their transport velocity with respect to groundwater flow velocity. An additional approach is provided by the filter theory.

Effects of body temperature on post-anoxic oxidative stress from the perspective of postnatal physiological adaptive processes in rats.

PubMed

Kletkiewicz, H; Rogalska, J; Nowakowska, A; Wozniak, A; Mila-Kierzenkowska, C; Caputa, M

2016-04-01

It is well known that decrease in body temperature provides protection to newborns subjected to anoxia/ischemia. We hypothesized that the normal body temperature of 33°C in neonatal rats (4°C below normal body temperature in adults) is in fact a preadaptation to protect CNS from anoxia and further reductions as well as elevations in temperature may be counterproductive. Our experiments aimed to examine the effect of changes in body temperature on oxidative stress development in newborn rats exposed to anoxia. Two-day-old Wistar rats were divided into 4 temperature groups: i. hypothermic at body temperature of 31°C, ii. maintaining physiological neonatal body temperature of 33°C, iii. forced to maintain hyperthermic temperature of 37°C, and i.v. forced to maintain hyperthermic temperature of 39°C. The temperature was controlled starting 15 minutes before and afterword during 10 minutes of anoxia as well as for 2 hours post-anoxia. Cerebral concentrations of lipid peroxidation products malondialdehyde (MDA) and conjugated dienes (CD) and the activities of antioxidant enzymes had been determined post mortem: immediately after anoxia was finished and 3, 7, and 14 days later. There were no post-anoxic changes in the concentration of MDA, CD and in antioxidant enzymes activity in newborn rats kept at their physiological body temperature of 33°C. In contrast, perinatal anoxia at body temperature elevated to 37°C or 39°C as well as under hypothermic conditions (31°C) intensified post-anoxic oxidative stress and depleted the antioxidant pool. Overall, these findings suggest that elevated body temperature (hyperthermia or fever), as well as exceeding cooling beyond the physiological level of body temperature of newborn rats, may extend perinatal anoxia-induced brain lesions. Our findings provide new insights into the role of body temperature in anoxic insult in vivo.

Isotope studies of carbonate rocks of La Luna Formation (Venezuela) to constrain the oceanic anoxic event 3 (OAE3)

NASA Astrophysics Data System (ADS)

Machado, M. C.; Chemale, F., Jr.; Kawashita, K.; Rey, O.; Moura, C. A. V.

2016-12-01

87Sr/86Sr ratios, δ13C, and δ18O determinations performed on 30 bulk carbonate rocks are presented to constrain the isotope characteristics regarding Oceanic Anoxic Event 3 in the La Luna Formation, Maracaibo Basin. The samples were collected along a 22 m profile in San Miguel region (Merida State, Venezuela). The exhibited 87Sr/86Sr ratios are between 0.707659, at the base, and 0.707733 at the top of studied section, corresponding estimated younger numerical ages than the inferred ages dated as Santonian (85.8-83.5 Ma) based on occurrence of Dicarinella asymetrica. The obtained 87Sr/86Sr ratios are certainly higher than expected for Santonian sea Sr and they are attributed to regular riverine strontium fluxes in the restricted (gulf-like) Maracaibo Basin. The values of δ18O data between -3.76‰ and -11.76‰ are distributed in two distinct clusters in a same way and coherent as for δ13C data which are in a range between -1.75‰ and -13.87‰. One of the clusters δ13C = -2.5 ± 1.0‰ and δ18O = -10.0 ± 1.5‰), illustrate the homogeneous marine deposition under tropical conditions, while the other, more variable, probably could reflect the cyclicity of temporally changes in Pacific versus Atlantic Ocean circulation with cooling water or cooling trend climate. These δ13C values around -2.5 ± 1.0‰ do not fit with the significant carbon isotope excursion as expected for the oceanic anoxic event (OAE) and support the work hypothesis that Coniacian-Santonian anoxic event (denominate as OAE3) is not a global one.

Magnetotactic bacteria in marine sediments: clues from recent cores from Brazilian Coast

NASA Astrophysics Data System (ADS)

Jovane, L.; Pellizari, V. H.; Brandini, F. P.; Braga, E. D. S.; Freitas, G. R.; Benites, M.; Rodelli, D.; Giorgioni, M.; Iacoviello, F.; Ruffato, D. G.; Lins, U.

2014-12-01

The magnetic properties (first order reversal curves, ferromagnetic resonance and decomposition of saturation remanent magnetization acquisition) of marine magnetotactic bacteria, in conjunction with geophysical, geochemical and oceanographic data from the Brazilian Coast, provide interesting insights regarding the primary productivity distribution in oceans. This finding suggests that magnetite produced by some magnetotactic bacteria retains magnetic properties in relation to the crystallographic structure of the magnetic phase produced and thus might represent a "magnetic fingerprint" for the presence of magnetotactic bacteria. The use of those magnetic properties is a non-destructive, new technology that might allow for the identification and presence of specific species or types of magnetotactic bacteria in certain environments such as sediment. We will also show some preliminary results on the biogeochemical factors that control magnetotactic bacterial populations, documenting the environment and the preservation of bacterial magnetite, which dominates the palaeomagnetic signal throughout recent sediments from Brazilian Coast. We searched for magnetotactic bacteria in order to understand the ecosystems and environmental change related to their presence in sediments. We studied magnetotactic bacterial concentration and geophysical, geochemical and oceanographic results in marine settings measuring crucially nutrients availability in the water column and in sediments, on particulate delivery to the seafloor, to understand the environmental condition that allow the presence of magnetotactic bacteria and magnetosomes in sediments.

Event extraction of bacteria biotopes: a knowledge-intensive NLP-based approach

PubMed Central

2012-01-01

Background Bacteria biotopes cover a wide range of diverse habitats including animal and plant hosts, natural, medical and industrial environments. The high volume of publications in the microbiology domain provides a rich source of up-to-date information on bacteria biotopes. This information, as found in scientific articles, is expressed in natural language and is rarely available in a structured format, such as a database. This information is of great importance for fundamental research and microbiology applications (e.g., medicine, agronomy, food, bioenergy). The automatic extraction of this information from texts will provide a great benefit to the field. Methods We present a new method for extracting relationships between bacteria and their locations using the Alvis framework. Recognition of bacteria and their locations was achieved using a pattern-based approach and domain lexical resources. For the detection of environment locations, we propose a new approach that combines lexical information and the syntactic-semantic analysis of corpus terms to overcome the incompleteness of lexical resources. Bacteria location relations extend over sentence borders, and we developed domain-specific rules for dealing with bacteria anaphors. Results We participated in the BioNLP 2011 Bacteria Biotope (BB) task with the Alvis system. Official evaluation results show that it achieves the best performance of participating systems. New developments since then have increased the F-score by 4.1 points. Conclusions We have shown that the combination of semantic analysis and domain-adapted resources is both effective and efficient for event information extraction in the bacteria biotope domain. We plan to adapt the method to deal with a larger set of location types and a large-scale scientific article corpus to enable microbiologists to integrate and use the extracted knowledge in combination with experimental data. PMID:22759462

Event extraction of bacteria biotopes: a knowledge-intensive NLP-based approach.

PubMed

Ratkovic, Zorana; Golik, Wiktoria; Warnier, Pierre

2012-06-26

Bacteria biotopes cover a wide range of diverse habitats including animal and plant hosts, natural, medical and industrial environments. The high volume of publications in the microbiology domain provides a rich source of up-to-date information on bacteria biotopes. This information, as found in scientific articles, is expressed in natural language and is rarely available in a structured format, such as a database. This information is of great importance for fundamental research and microbiology applications (e.g., medicine, agronomy, food, bioenergy). The automatic extraction of this information from texts will provide a great benefit to the field. We present a new method for extracting relationships between bacteria and their locations using the Alvis framework. Recognition of bacteria and their locations was achieved using a pattern-based approach and domain lexical resources. For the detection of environment locations, we propose a new approach that combines lexical information and the syntactic-semantic analysis of corpus terms to overcome the incompleteness of lexical resources. Bacteria location relations extend over sentence borders, and we developed domain-specific rules for dealing with bacteria anaphors. We participated in the BioNLP 2011 Bacteria Biotope (BB) task with the Alvis system. Official evaluation results show that it achieves the best performance of participating systems. New developments since then have increased the F-score by 4.1 points. We have shown that the combination of semantic analysis and domain-adapted resources is both effective and efficient for event information extraction in the bacteria biotope domain. We plan to adapt the method to deal with a larger set of location types and a large-scale scientific article corpus to enable microbiologists to integrate and use the extracted knowledge in combination with experimental data.

Thermal control of virulence factors in bacteria: A hot topic

PubMed Central

Lam, Oliver; Wheeler, Jun; Tang, Christoph M

2014-01-01

Pathogenic bacteria sense environmental cues, including the local temperature, to control the production of key virulence factors. Thermal regulation can be achieved at the level of DNA, RNA or protein and although many virulence factors are subject to thermal regulation, the exact mechanisms of control are yet to be elucidated in many instances. Understanding how virulence factors are regulated by temperature presents a significant challenge, as gene expression and protein production are often influenced by complex regulatory networks involving multiple transcription factors in bacteria. Here we highlight some recent insights into thermal regulation of virulence in pathogenic bacteria. We focus on bacteria which cause disease in mammalian hosts, which are at a significantly higher temperature than the outside environment. We outline the mechanisms of thermal regulation and how understanding this fundamental aspect of the biology of bacteria has implications for pathogenesis and human health. PMID:25494856

Anaerobic bacteria

MedlinePlus

Anaerobic bacteria are bacteria that do not live or grow when oxygen is present. In humans, these bacteria ... Brook I. Diseases caused by non-spore-forming anaerobic bacteria. In: Goldman L, Schafer AI, eds. Goldman-Cecil ...

Diverse antimicrobial interactions of halophilic archaea and bacteria extend over geographical distances and cross the domain barrier

PubMed Central

Atanasova, Nina S; Pietilä, Maija K; Oksanen, Hanna M

2013-01-01

The significance of antimicrobial substances, halocins, produced by halophilic archaea and bacteria thriving in hypersaline environments is relatively unknown. It is suggested that their production might increase species diversity and give transient competitive advances to the producer strain. Halocin production is considered to be common among halophilic archaea, but there is a lack of information about halocins produced by bacteria in highly saline environments. We studied the antimicrobial activity of 68 halophilic archaea and 22 bacteria isolated from numerous geographically distant hypersaline environments. Altogether 144 antimicrobial interactions were found between the strains and aside haloarchaea, halophilic bacteria from various genera were identified as halocin producers. Close to 80% of the interactions were detected between microorganisms from different genera and in few cases, even across the domain boundary. Several of the strains produced halocins with a wide inhibitory spectrum as has been observed before. Most of the antimicrobial interactions were found between strains from distant sampling sites indicating that hypersaline environments around the world have similar microorganisms with the potential to produce wide activity range antimicrobials. PMID:23929527

Advances in methods for detection of anaerobic ammonium oxidizing (anammox) bacteria.

PubMed

Li, Meng; Gu, Ji-Dong

2011-05-01

Anaerobic ammonium oxidation (anammox), the biochemical process oxidizing ammonium into dinitrogen gas using nitrite as an electron acceptor, has only been recognized for its significant role in the global nitrogen cycle not long ago, and its ubiquitous distribution in a wide range of environments has changed our knowledge about the contributors to the global nitrogen cycle. Currently, several groups of methods are used in detection of anammox bacteria based on their physiological and biochemical characteristics, cellular chemical composition, and both 16S rRNA gene and selective functional genes as biomarkers, including hydrazine oxidoreductase and nitrite reductase encoding genes hzo and nirS, respectively. Results from these methods coupling with advances in quantitative PCR, reverse transcription of mRNA genes and stable isotope labeling have improved our understanding on the distribution, diversity, and activity of anammox bacteria in different environments both natural and engineered ones. In this review, we summarize these methods used in detection of anammox bacteria from various environments, highlight the strengths and weakness of these methods, and also discuss the new development potentials on the existing and new techniques in the future.

Transport, anoxia and energy control on anaerobic respiration and methanogenesis in anoxic peat soils

NASA Astrophysics Data System (ADS)

Bonaiuti, Simona; Blodau, Christian; Knorr, Klaus-Holger

2017-04-01

In deep and permanently water saturated peat deposits, extremely low diffusive transport and concomitant build-up of metabolic end-products, i.e of dissolved inorganic carbon (DIC) and methane (CH4), have been found to slow-down anaerobic respiration and methanogenesis. Such accumulation of DIC and CH4 lowers the Gibbs free energy yield of terminal respiration and methanogenesis, which can inhibit the course of anaerobic metabolic processes. In particular, this affects terminal steps of the breakdown of organic carbon (C), such as methanogenesis, acetogenesis and fermentation processes, which occur near thermodynamic minimum energy thresholds. This effect is thus of critical importance for the long-term C sequestration, as the slow-down of decomposition ultimately regulates the long-term fate of C in deep peat deposits. The exact controls of this observed slow-down of organic matter mineralization are not yet fully understood. Moreover, altered patterns of water or gas transport due to predicted changes in climate may affect these controls in peat soils. Therefore, the aim of this study was to investigate how burial of peat leads to an inactivation of anaerobic decomposition and to investigate the effects of advective water transport and persistently anoxic conditions on anaerobic decomposition, temporal evolution of thermodynamic energy yields to methanogenesis and methanogenic pathways. To this end, we conducted a column experiment with homogenized, ombrotrophic peat over a period of 300 days at 20˚ C. We tested i) a control treatment under diffusive transport only, ii) an advective flow treatment with a flow of 10 mm d-1, and iv) an anoxic treatment to evaluate changes in decomposition in absence of oxygen in the unsaturated zone of the cores. A slow-down of anaerobic respiration and methanogenesis generally set in at larger depths after 150 days at CH4 concentrations of 0.6-0.9 mmol L-1 and DIC concentrations of 6-12 mmol L-1. This effect occurred at higher

Rapid Return of Nitrogen but not Phosphorus to Ecosystem Nutrition During Decomposition of Quagga Mussel Tissue in Sand, Mud, or Water During Oxic or Anoxic Incubation: Implications for Phytoplankton Bioenergetics.

NASA Astrophysics Data System (ADS)

Cooney, E. M.; Cuhel, R. L.; Aguilar, C.

2016-02-01

In 2003 Quagga mussels were found to have invaded Lake Michigan. Their presence has changed the structure of the lake both ecologically (benthification) as well as chemically (oligotrophication). They consume large amounts of phytoplankton, which decreases the particulate nitrogen and phosphorous nutrients available to other consumers including zooplankton. As a result, fisheries productivity has decreased nearly 95%. Recently reaching the end of the first life cycle, in death they release a portion of these nutrients back into the freshwater system during decomposition. This work determined amounts of phosphorus and nitrogen nutrient recycling for several relevant sediment-water interface conditions: oxic vs anoxic in water, mud, or sand over a weeklong period. Concentrations of ammonium, soluble reactive phosphorus, and nitrate were used to analyze nutrient release as decomposition took place. In a short time up to 25% of tissue N was released as ammonia, and under oxic conditions in mud or sand, nitrification converted some of the ammonia to nitrate. Unexpectedly, mussels decaying in anoxic conditions released ammonium much more slowly. A slower rate of release in ammonium for the intact body with the shell (burial) was observed when compared to ground mussel tissue (detritivory). Nitrate was removed in anoxic incubations, indicating anaerobic denitrification. Phosphate release was initially higher under anoxic conditions than those decaying aerobically. There was no significant difference in the amount or rate of release of SRP between ground mussel and whole bodied with the shell. The anoxic treatment showed similar patterns of release for both ground mussel and intact body with shell. Most important, phosphate was subsequently removed in all treatments and diffusible nutrient was minimal (<100nM). The results link to nutrient assimilation patterns of deep phytoplankton communities, which can replace nitrate with ammonium as an N source.

THE ANAEROBIC BIODEGRADATION OF O-,M- AND P-CRESOL BY SULFATE-REDUCING BACTERIAL ENRICHMENT CULTURES OBTAINED FROM A SHALLOW ANOXIC AQUIFER

EPA Science Inventory

Sulfate-reducing bacterial enrichments were obtained from a shallow anoxic aquifer for their ability to metabolize either o-, m-, orp-cresol. GC/MS and simultaneous adaptation experiments suggested that the anaerobic decomposition of p-cresol proceeds ...

Authigenic carbonate precipitation at the end-Guadalupian (Middle Permian) in China: Implications for the carbon cycle in ancient anoxic oceans

NASA Astrophysics Data System (ADS)

Saitoh, Masafumi; Ueno, Yuichiro; Isozaki, Yukio; Shibuya, Takazo; Yao, Jianxin; Ji, Zhansheng; Shozugawa, Katsumi; Matsuo, Motoyuki; Yoshida, Naohiro

2015-12-01

Carbonate precipitation is a major process in the global carbon cycle. It was recently proposed that authigenic carbonate (carbonate precipitated in situ at the sediment-water interface and/or within the sediment) played a major role in the carbon cycle throughout Earth's history. The carbon isotopic composition of authigenic carbonates in ancient oceans have been assumed to be significantly lower than that of dissolved inorganic carbon (DIC) in seawater, as is observed in the modern oceans. However, the δ13Ccarb values of authigenic carbonates in the past has not been analyzed in detail. Here, we report authigenic carbonates in the uppermost Guadalupian (Middle Permian) rocks at Chaotian, Sichuan, South China. Monocrystalline calcite crystals <20 mm long are common in the black mudstone/chert sequence that was deposited on a relatively deep anoxic slope/basin along the continental margin. Textures of the crystals indicate in situ precipitation on the seafloor and/or within the sediments. The calcite precipitation corresponds stratigraphically with denitrification and sulfate reduction in the anoxic deep-water mass, as indicated by previously reported nitrogen and sulfur isotope records, respectively. Relatively high δ13Ccarb values of the authigenic carbonates (largely -1 ‰) compared with those of organic matter in the rocks (ca. -26 ‰) suggest that the main carbon source of the carbonates was DIC in the water column. The calcite crystals precipitated in an open system with respect to carbonate, possibly near the sediment-water interface rather than deep within the sediments. The δ13Ccarb values of the carbonates were close to the δ13CDIC value of seawater due to mixing of 13C-depleted remineralized organic carbon (that was released into the water column by the water-mass anaerobic respiration) with the large DIC pool in the oceans. Our results imply that δ13Ccarb values of authigenic carbonates in the anoxic oceans might have been systematically

Antimicrobial-resistant bacteria in wild game in Slovenia

NASA Astrophysics Data System (ADS)

Križman, M.; Kirbiš, A.; Jamnikar-Ciglenečki, U.

2017-09-01

Wildlife is usually not exposed to clinically-used antimicrobial agents but can acquire antimicrobial resistance throughout contact with humans, domesticated animals and environments. Samples of faeces from intestines (80 in total) were collected from roe deer (52), wild boars (11), chamois (10) red deer (6) and moufflon (1). After culture on ChromID extended spectrum β-lactamase (ESBL) plates to select for growth of ESBL-producing bacteria, 25 samples produced bacterial colonies for further study. Six species of bacteria were identified from the 25 samples: Stenotrophomonas maltophilia, Serratia fonticola, Stenotrophomonas nitritireducens, Enterococcus faecium, Enterococcus faecalis and Escherichia coli. Two ESBL enzymes were amplified from group TEM and three from group CTX-M-1. Undercooked game meat and salami can be a source of resistant bacteria when animals are not eviscerated properly.

Exploring the potential of anaerobic sulfate reduction process in treating sulfonated diazo dye: Microbial community analysis using bar-coded pyrosequencing.

PubMed

Rasool, Kashif; Shahzad, Asif; Lee, Dae Sung

2016-11-15

Anaerobic decolorization and biotransformation of azo dye was investigated in a sulfate-reducing environment. Batch reactor studies were performed with mixed cultures of anaerobic sulfate-reducing bacteria (SRBs) enriched from anaerobic digester sludge. Complete sulfate and color removal were achieved in batch experiments with different initial dye concentrations (50-2500mg/L) and 1000mg/L of sulfate. Induction of various oxidoreductive enzyme activities such as phenol oxidase, veratryl alcohol oxidase, lignin peroxidase, and azo reductase was studied to understand their involvement in dye metabolism under anoxic environment. The degradation of Cotton Red B was confirmed using high-performance liquid chromatography and gas chromatography-mass spectroscopy. Sulfidogenic sludge demonstrated excellent dye degradation and mineralization ability, producing aniline and 1,4-diamino benzene as metabolites. A barcoded 16S rRNA gene-pyrosequencing approach was used to assess the bacterial diversity in the sludge culture and a phylogenetic tree was constructed for sulfate-reducing bacteria. Copyright © 2016 Elsevier B.V. All rights reserved.

[Metabolism of carbohydrates in the cells of green sulphur bacteria Chlorobium limicola Ya-2002].

PubMed

Horishnyĭ, M B; Hudz', S P; Hnatush, S O

2009-01-01

The nature of carbohydrates that accumulate in the cells of photosynthetic green sulphur bacteria of Chlorobium limicola Ya-2002 has been investigated. It is shown by infra-red spectrometry, that carbohydrates accumulated in the cells of bacteria are identical (by 90-95%) to glycogen of the bull liver. Exogenous glucose, saccharose, maltose, did not stimulate formation of glycogen. Growth of glycogen level in the cells of bacteria was observed at addition of acetate or piruvate in the conditions of bacteria cultivation in the light and in the presence CO2 and H2S in the environment. Washed cells of C. limicola Ya-2002 did not use glucose of the environment neither in the conditions of illumination nor in darkness, however acetate and piruvate are actively used in the light. During incubation of the washed cells in darkness the level of glycogen fell down approximately three times. Its amount during cells incubation in the light did not change. The decline of glycogen level in cells during their incubation in darkness was accompanied by piling up of carbonic acids in the environment acetate prevailing among them.

Sociomicrobiology and Pathogenic Bacteria.

PubMed

Xavier, Joao B

2016-06-01

The study of microbial pathogenesis has been primarily a reductionist science since Koch's principles. Reductionist approaches are essential to identify the causal agents of infectious disease, their molecular mechanisms of action, and potential drug targets, and much of medicine's success in the treatment of infectious disease stems from that approach. But many bacteria-caused diseases cannot be explained by a single bacterium. Several aspects of bacterial pathogenesis will benefit from a more holistic approach that takes into account social interaction among bacteria of the same species and between species in consortia such as the human microbiome. The emerging discipline of sociomicrobiology provides a framework to dissect microbial interactions in single and multi-species communities without compromising mechanistic detail. The study of bacterial pathogenesis can benefit greatly from incorporating concepts from other disciplines such as social evolution theory and microbial ecology, where communities, their interactions with hosts, and with the environment play key roles.

Assessing the Record of Anoxic/Dysoxic Events in Lower Aptian Cupido/La Peña Formations, Northeastern Mexico

NASA Astrophysics Data System (ADS)

Maurrasse, F. J.; Barragan-Manzo, R.; Ponton, C.

2008-05-01

-thick each that are remarkably devoid of benthic foraminifers. They occur at 5. 72 m, 11.45m and 29.6 m, respectively, below the La Peña Fm. Variations within the Cupido Fm are consistent with fluctuating high- productivity, well-oxygenated neritic environment punctuated by development of hypoxic to anoxic bottom waters (Maurrasse et al., 2006). These recurrent episodes of severe oxygen depletion fall within the time interval that may be correlational with the infrajacent D. deshayesi to possibly the D. wessi zones in the Mediterranean ammonite biozonation scheme. We interpret these horizons to represent recurrent hypoxic to anoxic bottom conditions that are local expression of global forcing factors during Cretaceous greenhouse conditions that lead to well-defined OAE-1a and the subsequent anoxic events. Barragan-Manzo, R., and Maurrasse, F., (2008) Revista Mexicana de Ciencias Geologicas, v. 25, 1, p. 145-157. Barragan-Manzo, R., and Mendez-Franco, 2005, Towards a standard ammonite zonation for the Aptian (Lower Cretaceous) of northern Mexico. Revista Mexicana de Ciencias Geologicas, v. 22, 1, p. 39-47. Maurrasse, F. J-M. R., Barragan-Manzo, R., and Ponton, C. 2006, Cupido- La Peña Formations: High-Productivity to Super-Productivity during the Cretaceous Enhanced Greenhouse Conditions, GSA Abst.with programs v. 38, no 7, p. 491.

Numerical taxonomy of heavy metal tolerant bacteria isolated from the estuarine environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allen, D.A.; Austin, B.; Mills, A.L.

1977-01-01

Metal tolerant bacteria, totalling 301 strains, were isolated from water and sediment samples collected from Chesapeake Bay. Growth in the presence of 100 ppm cadmium, chromium, cobalt, lead, mercury and molybdenum was tested. In addition, the strains were examined for 118 biochemical, cultural, morphological, nutritional and physiological, characters and the data were analyzed by computer, using the simple matching and Jaccard coefficients. From sorted similarity matrices, 293 strains, 97% of the total, were removed in 12 clusters defined at the 80 to 85% similarity level. The clusters included Bacillus and Pseudomonas spp. and genera and species of Enterobacteriaceae. Three clusters,more » containing gram negative rods, were not identified. Several of the clusters were composed of strains exhibiting tolerance to a wide range of heavy metals, whereas three of the clusters contained bacteria that were capable of growth in the presence of only a few of the metals examined in this study. Antibiotic resistance of the metal resistant strains has also been examined.« less

Multidrug resistance in enteric and other gram-negative bacteria.

PubMed

George, A M

1996-05-15

In Gram-negative bacteria, multidrug resistance is a term that is used to describe mechanisms of resistance by chromosomal genes that are activated by induction or mutation caused by the stress of exposure to antibiotics in natural and clinical environments. Unlike plasmid-borne resistance genes, there is no alteration or degradation of drugs or need for genetic transfer. Exposure to a single drug leads to cross-resistance to many other structurally and functionally unrelated drugs. The only mechanism identified for multidrug resistance in bacteria is drug efflux by membrane transporters, even though many of these transporters remain to be identified. The enteric bacteria exhibit mostly complex multidrug resistance systems which are often regulated by operons or regulons. The purpose of this review is to survey molecular mechanisms of multidrug resistance in enteric and other Gram-negative bacteria, and to speculate on the origins and natural physiological functions of the genes involved.

A new step aeration approach towards the improvement of nitrogen removal in a full scale Carrousel oxidation ditch.

PubMed

Jin, Pengkang; Wang, Xianbao; Wang, Xiaochang; Ngo, Huu Hao; Jin, Xin

2015-12-01

Two aeration modes, step aeration and point aeration, were used in a full-scale Carrousel oxidation ditch with microporous aeration. The nitrogen removal performance and mechanism were analyzed. With the same total aeration input, both aeration modes demonstrated good nitrification outcomes with the average efficiency in removing NH4(+)-N of more than 98%. However, the average removal efficiencies for total nitrogen were 89.3% and 77.6% under step aeration and point aeration, respectively. The results indicated that an extended aerobic zone followed the aeration zones could affect the proportion of anoxic and oxic zones. The step aeration with larger anoxic zones indicated better TN removal efficiency. More importantly, step aeration provided the suitable environment for both nitrifiers and denitrifiers. The diversity and relative abundance of denitrifying bacteria under the step aeration (1.55%) was higher than that under the point aeration (1.12%), which resulted in an overall higher TN removal efficiency. Copyright © 2015 Elsevier Ltd. All rights reserved.

Anoxic deep-sea microbial dolomite as a paleoceanographic archive - new insights from old "bugs"

NASA Astrophysics Data System (ADS)

Miller, N. R.; Leybourne, M. I.

2010-12-01

Earth’s history of biogenic carbonate production is dominated by pre-skeletal (late Ediacaran) microbe-catalyzed carbonate, including low T/P microbial (aka organogenic) dolomite, but paleoceanographic contexts are unclear due to the lack of proxy control provided by skeletal analogs and/or diagenesis. Microbial communities affiliated with dolomite generation (chiefly sulfate reducers and methanogens) are now known to persist in a diversity of Recent anoxic environments, but only deep-sea settings are sufficiently insulated from eustatic-meteoric diagenesis to preserve long-term records of possible paleoceanographic significance. The Miocene Monterey Formation contains episodic-to-cyclic microbial dolomite intervals interstratified with microfossil calcite, and thereby offers an excellent test the paleoceoanographic archive potential of microbial dolomite. Accordingly, we established a detailed dolomite chemostratigraphic profile (δ18O, δ13C, TOC, trace elements/REEs) from a continuous, thermally immature, Monterey core (offshore Santa Barbara-Ventura Basin), preserving >100 distinct early diagenetic (pre significant compaction, pre-diatom dissolution, post-pyrite) microbial dolomite intervals. Despite dolomite horizons being physically separate from one stratum to the next, they exhibit regular core-wide variations in δ13C and δ18O. Dolomite within the main Monterey depositional interval has entirely negative δ13C values (-2 to -16‰) consistent with generation in the zone of microbial sulfate reduction, whereas positive δ13C values (+2 to +9‰) consistent with generation from methanogenic pore-waters occur in lithologic transitions with bounding formations. Dolomites within the main Monterey depositional interval mirror microfossil calcite δ18O variations, notably pronounced global mid-Miocene enrichment after ~14 Ma linked to cooling and significant expansion of Antarctic ice. Dolomite δ13C mirrors sediment accumulation rate, with lightest values

Potential sources of bacteria colonizing the cryoconite of an Alpine glacier

PubMed Central

Franzetti, Andrea; Navarra, Federico; Tagliaferri, Ilario; Gandolfi, Isabella; Bestetti, Giuseppina; Minora, Umberto; Azzoni, Roberto Sergio; Diolaiuti, Guglielmina; Smiraglia, Claudio

2017-01-01

We investigated the potential contribution of ice-marginal environments to the microbial communities of cryoconite holes, small depressions filled with meltwater that form on the surface of Forni Glacier (Italian Alps). Cryoconite holes are considered the most biologically active environments on glaciers. Bacteria can colonize these environments by short-range transport from ice-marginal environments or by long-range transport from distant areas. We used high throughput DNA sequencing to identify Operational Taxonomic Units (OTUs) present in cryoconite holes and three ice-marginal environments, the moraines, the glacier forefield, and a large (> 3 m high) ice-cored dirt cone occurring on the glacier surface. Bacterial communities of cryoconite holes were different from those of ice-marginal environments and hosted fewer OTUs. However, a network analysis revealed that the cryoconite holes shared more OTUs with the moraines and the dirt cone than with the glacier forefield. Ice-marginal environments may therefore act as sources of bacteria for cryoconite holes, but differences in environmental conditions limit the number of bacterial strains that may survive in them. At the same time, cryoconite holes host a few OTUs that were not found in any ice-marginal environment we sampled, thus suggesting that some bacterial populations are positively selected by the specific environmental conditions of the cryoconite holes. PMID:28358872

Potential sources of bacteria colonizing the cryoconite of an Alpine glacier.

PubMed

Franzetti, Andrea; Navarra, Federico; Tagliaferri, Ilario; Gandolfi, Isabella; Bestetti, Giuseppina; Minora, Umberto; Azzoni, Roberto Sergio; Diolaiuti, Guglielmina; Smiraglia, Claudio; Ambrosini, Roberto

2017-01-01

We investigated the potential contribution of ice-marginal environments to the microbial communities of cryoconite holes, small depressions filled with meltwater that form on the surface of Forni Glacier (Italian Alps). Cryoconite holes are considered the most biologically active environments on glaciers. Bacteria can colonize these environments by short-range transport from ice-marginal environments or by long-range transport from distant areas. We used high throughput DNA sequencing to identify Operational Taxonomic Units (OTUs) present in cryoconite holes and three ice-marginal environments, the moraines, the glacier forefield, and a large (> 3 m high) ice-cored dirt cone occurring on the glacier surface. Bacterial communities of cryoconite holes were different from those of ice-marginal environments and hosted fewer OTUs. However, a network analysis revealed that the cryoconite holes shared more OTUs with the moraines and the dirt cone than with the glacier forefield. Ice-marginal environments may therefore act as sources of bacteria for cryoconite holes, but differences in environmental conditions limit the number of bacterial strains that may survive in them. At the same time, cryoconite holes host a few OTUs that were not found in any ice-marginal environment we sampled, thus suggesting that some bacterial populations are positively selected by the specific environmental conditions of the cryoconite holes.

Bacteria from diverse habitats colonize and compete in the mouse gut.

PubMed

Seedorf, Henning; Griffin, Nicholas W; Ridaura, Vanessa K; Reyes, Alejandro; Cheng, Jiye; Rey, Federico E; Smith, Michelle I; Simon, Gabriel M; Scheffrahn, Rudolf H; Woebken, Dagmar; Spormann, Alfred M; Van Treuren, William; Ursell, Luke K; Pirrung, Megan; Robbins-Pianka, Adam; Cantarel, Brandi L; Lombard, Vincent; Henrissat, Bernard; Knight, Rob; Gordon, Jeffrey I

2014-10-09

To study how microbes establish themselves in a mammalian gut environment, we colonized germ-free mice with microbial communities from human, zebrafish, and termite guts, human skin and tongue, soil, and estuarine microbial mats. Bacteria from these foreign environments colonized and persisted in the mouse gut; their capacity to metabolize dietary and host carbohydrates and bile acids correlated with colonization success. Cohousing mice harboring these xenomicrobiota or a mouse cecal microbiota, along with germ-free "bystanders," revealed the success of particular bacterial taxa in invading guts with established communities and empty gut habitats. Unanticipated patterns of ecological succession were observed; for example, a soil-derived bacterium dominated even in the presence of bacteria from other gut communities (zebrafish and termite), and human-derived bacteria colonized germ-free bystander mice before mouse-derived organisms. This approach can be generalized to address a variety of mechanistic questions about succession, including succession in the context of microbiota-directed therapeutics. Copyright © 2014 Elsevier Inc. All rights reserved.

Diversity, community structure, and bioremediation potential of mercury-resistant marine bacteria of estuarine and coastal environments of Odisha, India.

PubMed

Dash, Hirak R; Das, Surajit

2016-04-01

Both point and non-point sources increase the pollution status of mercury and increase the population of mercury-resistant marine bacteria (MRMB). They can be targeted as the indicator organism to access marine mercury pollution, besides utilization in bioremediation. Thus, sediment and water samples were collected for 2 years (2010-2012) along Odisha coast of Bay of Bengal, India. Mercury content of the study sites varied from 0.47 to 0.99 ppb irrespective of the seasons of sampling. A strong positive correlation was observed between mercury content and MRMB population (P < 0.05) suggesting the utilization of these bacteria to assess the level of mercury pollution in the marine environment. Seventy-eight percent of the MRMB isolates were under the phylum Firmicutes, and 36 and 31% of them could resist mercury by mer operon-mediated volatilization and mercury biosorption, respectively. In addition, most of the isolates could resist a number of antibiotics and toxic metals. All the MRMB isolates possess the potential of growth and survival at cardinal pH (4-8), temperature (25-37 °C), and salinity (5-35 psu). Enterobacteria repetitive intergenic consensus (ERIC) and repetitive element palindromic PCR (REP-PCR) produced fingerprints corroborating the results of 16S rRNA gene sequencing. Fourier transform infrared (FTIR) spectral analysis also revealed strain-level speciation and phylogenetic relationships.

Pediatric Cystic Fibrosis Sputum Can Be Chemically Dynamic, Anoxic, and Extremely Reduced Due to Hydrogen Sulfide Formation

PubMed Central

Cowley, Elise S.; Kopf, Sebastian H.; LaRiviere, Alejandro

2015-01-01

ABSTRACT Severe and persistent bacterial lung infections characterize cystic fibrosis (CF). While several studies have documented the microbial diversity within CF lung mucus, we know much less about the inorganic chemistry that constrains microbial metabolic processes and their distribution. We hypothesized that sputum is chemically heterogeneous both within and between patients. To test this, we measured microprofiles of oxygen and sulfide concentrations as well as pH and oxidation-reduction potentials in 48 sputum samples from 22 pediatric patients with CF. Inorganic ions were measured in 20 samples from 12 patients. In all cases, oxygen was depleted within the first few millimeters below the sputum-air interface. Apart from this steep oxycline, anoxia dominated the sputum environment. Different sputum samples exhibited a broad range of redox conditions, with either oxidizing (16 mV to 355 mV) or reducing (−300 to −107 mV) potentials. The majority of reduced samples contained hydrogen sulfide and had a low pH (2.9 to 6.5). Sulfide concentrations increased at a rate of 0.30 µM H2S/min. Nitrous oxide was detected in only one sample that also contained sulfide. Microenvironmental variability was observed both within a single patient over time and between patients. Modeling oxygen dynamics within CF mucus plugs indicates that anoxic zones vary as a function of bacterial load and mucus thickness and can occupy a significant portion of the mucus volume. Thus, aerobic respiration accounts only partially for pathogen survival in CF sputum, motivating research to identify mechanisms of survival under conditions that span fluctuating redox states, including sulfidic environments. PMID:26220964

The Tonian Beck Spring Dolomite: Marine dolomitization in a shallow, anoxic sea

NASA Astrophysics Data System (ADS)

Shuster, Alice Mary; Wallace, Malcolm William; van Smeerdijk Hood, Ashleigh; Jiang, Ganqing

2018-06-01

The reason for the abundance of dolomite lithologies in Earth's early geological record compared to modern environments remains contentious. This study provides new insight into this Precambrian "dolomite problem" by revisiting one of the most controversial dolomite localities, the Beck Spring Dolomite, of Death Valley, USA. Consistent with some previous studies, petrographic evidence indicates that although the Beck Spring Dolomite now consists almost entirely of dolomite, it was originally precipitated largely as aragonite and high-Mg calcite. Depositional constituents (microbialites and ooids) were likely originally aragonitic, and early marine length-fast cements (now dolomite) are suggested to have precipitated as high-Mg calcite then replaced syntaxially by dolomite. Based on petrographic and geochemical evidence, we suggest that marine dolomitization was the dominant synsedimentary diagenetic process in the unit, and for the most part, involved syntaxial and mimetic replacement. Further, a length-slow fibrous dolomite generation was precipitated during the later stages of marine diagenesis as a primary marine dolomite cement. This is indicated by the length-slow crystallographic structure of the cement and from its preserved geochemical and cathodoluminescence growth zonation. This new evidence for Tonian marine dolomite precipitation reinforces the idea of Precambrian marine environmental conditions, including the chemical composition of seawater, promoting dolomite formation at this time. The trace metal geochemical composition of well-preserved marine components, especially dolomite marine cements, reveals information about redox conditions in this Tonian shallow seawater. In terms of rare earth element geochemistry, the Beck Spring Dolomite has no significant Ce anomaly, and a ubiquitous positive Eu anomaly, consistent with widespread oceanic anoxia during deposition. Furthermore, the relatively low levels of iron and chalcophile elements Co, Cu, Pb and

Distribution of iron- and sulfate-reducing bacteria across a coastal acid sulfate soil (CASS) environment: implications for passive bioremediation by tidal inundation.

PubMed

Ling, Yu-Chen; Bush, Richard; Grice, Kliti; Tulipani, Svenja; Berwick, Lyndon; Moreau, John W

2015-01-01

Coastal acid sulfate soils (CASS) constitute a serious and global environmental problem. Oxidation of iron sulfide minerals exposed to air generates sulfuric acid with consequently negative impacts on coastal and estuarine ecosystems. Tidal inundation represents one current treatment strategy for CASS, with the aim of neutralizing acidity by triggering microbial iron- and sulfate-reduction and inducing the precipitation of iron-sulfides. Although well-known functional guilds of bacteria drive these processes, their distributions within CASS environments, as well as their relationships to tidal cycling and the availability of nutrients and electron acceptors, are poorly understood. These factors will determine the long-term efficacy of "passive" CASS remediation strategies. Here we studied microbial community structure and functional guild distribution in sediment cores obtained from 10 depths ranging from 0 to 20 cm in three sites located in the supra-, inter- and sub-tidal segments, respectively, of a CASS-affected salt marsh (East Trinity, Cairns, Australia). Whole community 16S rRNA gene diversity within each site was assessed by 454 pyrotag sequencing and bioinformatic analyses in the context of local hydrological, geochemical, and lithological factors. The results illustrate spatial overlap, or close association, of iron-, and sulfate-reducing bacteria (SRB) in an environment rich in organic matter and controlled by parameters such as acidity, redox potential, degree of water saturation, and mineralization. The observed spatial distribution implies the need for empirical understanding of the timing, relative to tidal cycling, of various terminal electron-accepting processes that control acid generation and biogeochemical iron and sulfur cycling.

Bacteria, fungi and protozoa paper

EPA Pesticide Factsheets

Bacteria and fungi in source and treated drinking waterThis dataset is associated with the following publication:King , D., S. Pfaller , M. Donohue , S. Vesper , E. Villegas , M. Ware , S. Glassmeyer , M. Vogal, E. Furlong, and D. Kolpin. Microbial pathogens in source and treated waters from drinking water treatment plants in the United States and implications for human health. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 562: 987–995, (2016).

The role of natural environments in the evolution of resistance traits in pathogenic bacteria.

PubMed

Martinez, Jose L

2009-07-22

Antibiotics are among the most valuable compounds used for fighting human diseases. Unfortunately, pathogenic bacteria have evolved towards resistance. One important and frequently forgotten aspect of antibiotics and their resistance genes is that they evolved in non-clinical (natural) environments before the use of antibiotics by humans. Given that the biosphere is mainly formed by micro-organisms, learning the functional role of antibiotics and their resistance elements in nature has relevant implications both for human health and from an ecological perspective. Recent works have suggested that some antibiotics may serve for signalling purposes at the low concentrations probably found in natural ecosystems, whereas some antibiotic resistance genes were originally selected in their hosts for metabolic purposes or for signal trafficking. However, the high concentrations of antibiotics released in specific habitats (for instance, clinical settings) as a consequence of human activity can shift those functional roles. The pollution of natural ecosystems by antibiotics and resistance genes might have consequences for the evolution of the microbiosphere. Whereas antibiotics produce transient and usually local challenges in microbial communities, antibiotic resistance genes present in gene-transfer units can spread in nature with consequences for human health and the evolution of environmental microbiota that are largely ignored.

Characterization of microbial arsenate reduction in the anoxic bottom waters of Mono Lake, California

USGS Publications Warehouse