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45 records · Page 3Linked to original sources

Bacterial dominance in subseafloor sediments characterized by methane hydrates

The degradation of organic carbon in subseafloor sediments on continental margins contributes to the largest reservoir of methane on Earth. Sediments in the Andaman Sea are composed of ~ 1% marine-derived organic carbon and biogenic methane is present. Our objective was to determine microbial abundance and diversity in sediments that transition the gas hydrate occurrence zone (GHOZ) in the Andaman Sea. Microscopic cell enumeration revealed that most sediment layers harbored relatively low microbial abundance (10 3 –10 5 cells cm −3 ). Archaea were never detected despite the use of both DNA- and lipid-based methods. Statistical analysis of terminal restriction fragment length polymorphisms revealed distinct microbial communities from above, within, and below the GHOZ, and GHOZ samples were correlated with a decrease in organic carbon. Primer-tagged pyrosequences of bacterial 16S rRNA genes showed that members of the phylum Firmicutes are predominant in all zones. Compared with other seafloor settings that contain biogenic methane, this deep subseafloor habitat has a unique microbial community and the low cell abundance detected can help to refine global subseafloor microbial abundance.

FEMS Microbiology Ecology

Bacterial and archaeal phylogenetic diversity of a cold sulfur-rich spring on the shoreline of Lake Erie, Michigan

Studies of sulfidic springs have provided new insights into microbial metabolism, groundwater biogeochemistry, and geologic processes. We investigated Great Sulphur Spring on the western shore of Lake Erie and evaluated the phylogenetic affiliations of 189 bacterial and 77 archaeal 16S rRNA gene sequences from three habitats: the spring origin (11-m depth), bacterial-algal mats on the spring pond surface, and whitish filamentous materials from the spring drain. Water from the spring origin water was cold, pH 6.3, and anoxic (H 2 , 5.4 nM; CH 4 , 2.70 ??M) with concentrations of S 2- (0.03 mM), SO 4 2- (14.8 mM), Ca 2+ (15.7 mM), and HCO 3 - (4.1 mM) similar to those in groundwater from the local aquifer. No archaeal and few bacterial sequences were >95% similar to sequences of cultivated organisms. Bacterial sequences were largely affiliated with sulfur-metabolizing or chemolithotrophic taxa in Beta-, Gamma-, Delta-, and Epsilonproteobacteria. Epsilonproteobacteria sequences similar to those obtained from other sulfidic environments and a new clade of Cyanobacteria sequences were particularly abundant (16% and 40%, respectively) in the spring origin clone library. Crenarchaeota sequences associated with archaeal-bacterial consortia in whitish filaments at a German sulfidic spring were detected only in a similar habitat at Great Sulphur Spring. This study expands the geographic distribution of many uncultured Archaea and Bacteria sequences to the Laurentian Great Lakes, indicates possible roles for epsilonproteobacteria in local aquifer chemistry and karst formation, documents new oscillatorioid Cyanobacteria lineages, and shows that uncultured, cold-adapted Crenarchaeota sequences may comprise a significant part of the microbial community of some sulfidic environments. Copyright ?? 2009, American Society for Microbiology. All Rights Reserved.

Applied and Environmental Microbiology

Coupled arsenotrophy in a hot spring photosynthetic biofilm at Mono Lake, California

Red-pigmented biofilms grow on rock and cobble surfaces present in anoxic hot springs located on Paoha Island in Mono Lake. The bacterial community was dominated (∼ 85% of 16S rRNA gene clones) by sequences from the photosynthetic Ectothiorhodospira genus. Scraped biofilm materials incubated under anoxic conditions rapidly oxidized As(III) to As(V) in the light via anoxygenic photosynthesis but could also readily reduce As(V) to As(III) in the dark at comparable rates. Back-labeling experiments with 73 As(V) demonstrated that reduction to 73 As(III) also occurred in the light, thereby illustrating the cooccurrence of these two anaerobic processes as an example of closely coupled arsenotrophy. Oxic biofilms also oxidized As(III) to As(V). Biofilms incubated with [ 14 C]acetate oxidized the radiolabel to 14 CO 2 in the light but not the dark, indicating a capacity for photoheterotrophy but not chemoheterotrophy. Anoxic, dark-incubated samples demonstrated As(V) reduction linked to additions of hydrogen or sulfide but not acetate. Chemoautotrophy linked to As(V) as measured by dark fixation of [ 14 C]bicarbonate into cell material was stimulated by either H 2 or HS − . Functional genes for the arsenate respiratory reductase ( arrA ) and arsenic resistance ( arsB ) were detected in sequenced amplicons of extracted DNA, with about half of the arrA sequences closely related (∼98% translated amino acid identity) to those from the family Ectothiorhodospiraceae . Surprisingly, no authentic PCR products for arsenite oxidase ( aoxB ) were obtained, despite observing aerobic arsenite oxidation activity. Collectively, these results demonstrate close linkages of these arsenic redox processes occurring within these biofilms. Oxyanions of the group 15 element arsenic, arsenate [As(V)] and arsenite [As(III)], have been known for millennia to be potent poisons. Despite its well-established toxicity to life, the phenomenon of arsenic resistance was discovered whereby some microorganisms maintain an otherwise “normal” existence in the presence of high concentrations of As(V) or As(III) (17, 29, 31). More recently it has become recognized that certain representatives from the bacterial and archaeal domains can actually exploit the electrochemical potential of the As(V)/As(III) redox couple (+130 mV) to gain energy for growth. This can be achieved either by employing As(III) as an autotrophic electron donor or by using As(V) as a respiratory electron acceptor (18, 21, 34). The latter phenomenon, although most commonly associated with chemoheterotrophy, can also employ inorganic substances like sulfide or H 2 . Indeed, As(V)-respiring anaerobes displaying a capacity for chemoautotrophy with these electron donors have been isolated and described (5, 7, 16). We recently reported that photoautotrophy is supported by As(III) in anoxic biofilms located in hot springs on Paoha Island in Mono Lake, CA (15). This process represented a novel means of As(III) oxidation achieved via anoxygenic photosynthesis occurring in certain photosynthetic bacteria (i.e., Ectothiorhodospira ) and possibly within some cyanobacteria as well (e.g., “ Oscillatoria ”). Whether or not a microbial habitat is overtly oxic or anoxic, or temporally shifts between these two states over a diel cycle, critical energy linkages between aerobes and anaerobes have long been known for the biogeochemical cycles of key elements, such as sulfur, iron, and nitrogen. Most prominently studied is the case of nitrogen, whereby an ecological coupling exists between the processes of nitrification and denitrification (9, 10, 28). The former process provides energy to aerobic nitrifiers, while the latter process consumes the nitrate produced by this reaction, thereby meeting the energy needs of the denitrifiers. For arsenic, the detection of both As(III) oxidation and As(V) reduction in oxic and anoxic incubations of freshly collected periphyton suggested that an analogous coupled process may also occur for this element (12). Similarly, several uncontaminated soils in Japan displayed a capacity for either As(V) reduction or As(III) oxidation upon arsenic oxyanion amendment and whether they were incubated under oxic or anoxic conditions (39). A defined coculture consisting of an aerobic As(III) oxidizer (strain OL1) and an anaerobic As(V) respirer (strain Y5) was shown to function in this fashion under manipulated laboratory conditions of oxygen tension (26). We pursued the phenomenon of coupled arsenic metabolism further by using materials collected from the hot spring biofilms in Mono Lake, but we focused on examination of the cycling of arsenic under anoxic conditions. In this paper we report results obtained by manipulated incubations of red-pigmented biofilms found in the hot springs of Paoha Island. Preliminary community characterizations of these biofilms show that they are dominated by B acteria from the genus Ectothiorhodospira but also harbor an assemblage of Archaea related to the Halobacteriacaea . Incubation results have demonstrated the presence of the following arsenic metabolic activities: respiratory As(V) reduction, photosynthetic anaerobic As(III) oxidation, and aerobic As(III) oxidation, along with the ecophysiological conditions under which they occur. Surprisingly, we were unable to obtain authentic PCR products for arsenite oxidase genes ( aoxB ), despite observing aerobic As(III) oxidation activity. These biofilms serve as a model system for how anaerobic cycling of arsenic can be sustained with oxidation of As(III) by anoxygenic photosynthesis coupled to regeneration of this electron donor via dissimilatory As(V) reduction. The significance that such a light-driven anaerobic ecosystem may have played in the Archean Earth is discussed.

California

Microbial diversity in a hydrocarbon- and chlorinated-solvent- contaminated aquifer undergoing intrinsic bioremediation

A culture-independent molecular phylogenetic approach was used to survey constituents of microbial communities associated with an aquifer contaminated with hydrocarbons (mainly jet fuel) and chlorinated solvents undergoing intrinsic bioremediation. Samples were obtained from three redox zones: methanogenic, methanogenic-sulfate reducing, and iron or sulfate reducing. Small-subunit rRNA genes were amplified directly from aquifer material DNA by PCR with universally conserved or Bacteria - or Archaea -specific primers and were cloned. A total of 812 clones were screened by restriction fragment length polymorphisms (RFLP), approximately 50% of which were unique. All RFLP types that occurred more than once in the libraries, as well as many of the unique types, were sequenced. A total of 104 (94 bacterial and 10 archaeal) sequence types were determined. Of the 94 bacterial sequence types, 10 have no phylogenetic association with known taxonomic divisions and are phylogenetically grouped in six novel division level groups (candidate divisions WS1 to WS6); 21 belong to four recently described candidate divisions with no cultivated representatives (OP5, OP8, OP10, and OP11); and 63 are phylogenetically associated with 10 well-recognized divisions. The physiology of two particularly abundant sequence types obtained from the methanogenic zone could be inferred from their phylogenetic association with groups of microorganisms with a consistent phenotype. One of these sequence types is associated with the genus Syntrophus ; Syntrophus spp. produce energy from the anaerobic oxidation of organic acids, with the production of acetate and hydrogen. The organism represented by the other sequence type is closely related to Methanosaeta spp., which are known to be capable of energy generation only through aceticlastic methanogenesis. We hypothesize, therefore, that the terminal step of hydrocarbon degradation in the methanogenic zone of the aquifer is aceticlastic methanogenesis and that the microorganisms represented by these two sequence types occur in syntrophic association.

Applied and Environmental Microbiology

Impact of the dimethyl sulfoxide reductase superfamily on the evolution of biogeochemical cycles

The dimethyl sulfoxide reductase (or MopB) family is a diverse assemblage of enzymes found throughout Bacteria and Archaea . Many of these enzymes are believed to have been present in the last universal common ancestor (LUCA) of all cellular lineages. However, gaps in knowledge remain about how MopB enzymes evolved and how this diversification of functions impacted global biogeochemical cycles through geologic time. In this study, we perform maximum likelihood phylogenetic analyses on manually curated comparative genomic and metagenomic data sets containing over 47,000 distinct MopB homologs. We demonstrate that these enzymes constitute a catalytically and mechanistically diverse superfamily defined not by the molybdopterin- or tungstopterin-containing [molybdopterin or tungstopterin bis (pyranopterin guanine dinucleotide) (Mo/W- bis PGD)] cofactor but rather by the structural fold that binds it in the protein. Our results suggest that major metabolic innovations were the result of the loss of the metal cofactor or the gain or loss of protein domains. Phylogenetic analyses also demonstrated that formate oxidation and CO 2 reduction were the ancestral functions of the superfamily, traits that have been vertically inherited from the LUCA. Nearly all of the other families, which drive all other biogeochemical cycles mediated by this superfamily, originated in the bacterial domain. Thus, organisms from Bacteria have been the key drivers of catalytic and biogeochemical innovations within the superfamily. The relative ordination of MopB families and their associated catalytic activities emphasize fundamental mechanisms of evolution in this superfamily. Furthermore, it underscores the importance of prokaryotic adaptability in response to the transition from an anoxic to an oxidized atmosphere.

Microbiology Spectrum

Environmental controls on denitrifying communities and denitrification rates: Insights from molecular methods

The advent of molecular techniques has improved our understanding of the microbial communities responsible for denitrification and is beginning to address their role in controlling denitrification processes. There is a large diversity of bacteria, archaea, and fungi capable of denitrification, and their community composition is structured by long-term environmental drivers. The range of temperature and moisture conditions, substrate availability, competition, and disturbances have long-lasting legacies on denitrifier community structure. These communities may differ in physiology, environmental tolerances to pH and O 2 , growth rate, and enzyme kinetics. Although factors such as O 2 , pH, C availability, and NO 3 − pools affect instantaneous rates, these drivers act through the biotic community. This review summarizes the results of molecular investigations of denitrifier communities in natural environments and provides a framework for developing future research for addressing connections between denitrifier community structure and function.

Ecological Applications

Microbial ecology of deep-water mid-Atlantic canyons

The research described in this fact sheet will be conducted from 2012 to 2014 as part of the U.S. Geological Survey's DISCOVRE (DIversity, Systematics, and COnnectivity of Vulnerable Reef Ecosystems) Program. This integrated, multidisciplinary effort will be investigating a variety of topics related to unique and fragile deep-sea ecosystems from the microscopic level to the ecosystem level. One goal is to improve understanding, at the microbiological scale, of the benthic communities (including corals) that reside in and around mid-Atlantic canyon habitats and their associated environments. Specific objectives include identifying and characterizing the microbial associates of deep-sea corals, characterizing the microbial biofilms on hard substrates to better determine their role in engineering the ecosystem, and adding a microbial dimension to benthic community structure and function assessments by characterizing micro-eukaryotes, bacteria, and archaea in deep-sea sediments.

Fact Sheet

Survival of bacterial indicators and the functional diversity of native microbial communities in the Floridan aquifer system, south Florida

The Upper Floridan aquifer in the southern region of Florida is a multi-use, regional scale aquifer that is used as a potable water source and as a repository for passively recharged untreated surface waters, and injected treated surface water and wastewater, industrial wastes, including those which contain greenhouse gases (for example, carbon dioxide). The presence of confined zones within the Floridan aquifer that range in salinity from fresh to brackish allow regulatory agencies to permit the injection of these different types of product waters into specific zones without detrimental effects to humans and terrestrial and aquatic ecosystems. The type of recharge that has received the most regulatory attention in south Florida is aquifer storage and recovery (ASR). The treated water, prior to injection and during recovery, must meet primary and secondary drinking water standards. The primary microbiology drinking water standard is total coliforms, which have been shown to be difficult to inactivate below the regulatory standard during the treatment process at some ASR facilities. The inefficient inactivation of this group of indicator bacteria permits their direct injection into the storage zones of the Floridan aquifer. Prior to this study, the inactivation rates for any member of the total coliform group during exposure to native geochemical conditions in groundwater from any zone of the Floridan aquifer had not been derived. Aboveground flow through mesocosms and diffusion chambers were used to quantify the inactivation rates of two bacterial indicators, Escherichia coli and Pseudomonas aeruginosa, during exposure to groundwater from six wells. These wells collect water from two ASR storage zones: the Upper Floridan aquifer (UFA) and Avon Park Permeable Zone (APPZ). Both bacterial strains followed a biphasic inactivation model. The E. coli populations had slower inactivation rates in the UFA (range: 0.217–0.628 per hour (h -1 )) during the first phase of the model than when exposed to groundwater from the APPZ (range: 0.540–0.684 h -1 ). The inactivation rates for the first phase of the models for P. aeruginosa were not significantly different between the UFA (range: 0.144–0.770 h -1 ) and APPZ (range: 0.159–0.772 h -1 ) aquifer zones. The inactivation rates for the second phase of the model for this P. aeruginosa were also similar between UFA (range: 0.003–0.008 h -1 ) and APPZ (0.004–0.005 h -1 ) zones, although significantly slower than the model’s first phase rates for this bacterial species. Geochemical data were used to determine which dissimilatory biogeochemical reactions were most likely to occur under the native conditions in the UFA and APPZ zones using thermodynamics principles to calculate free energy yields and other cell-related energetics data. The biogeochemical processes of acetotrophic and hydrogenotrophic sulfate reduction, methanogenesis and anaerobic oxidation of methane dominated in all six groundwater sites. A high throughput DNA microarray sequencing technology was used to characterize the diversity in the native aquifer bacterial communities (bacteria and archaea) and assign putative physiological capabilities to the members of those communities. The bacterial communities in both zones of the aquifer were shown to possess the capabilities for primary and secondary fermentation, acetogenesis, methanogenesis, anaerobic methane oxidation, syntrophy with methanogens, ammonification, and sulfate reduction. The data from this study provide the first determination of bacterial indicator survival during exposure to native geochemical conditions of the Floridan aquifer in south Florida. Additionally, the energetics and functional bacterial diversity characterizations are the first descriptions of native bacterial communities in this region of the Floridan aquifer and reveal how these communities persist under such extreme conditions. Collectively, these types of data can be used to develop and refine groundwater models.

Florida

Broader impacts for ecologists: Biological soil crust as a model system for education

Biological soil crusts (biocrusts) are a complex community of algae, cyanobacteria, lichens, bryophytes, and assorted bacteria, fungi, archaea, and bacteriophages that colonize the soil surface. Biocrusts are particularly common in drylands and are found in arid and semiarid ecosystems worldwide. While diminutive in size, biocrusts often cover large terrestrial areas, provide numerous ecosystem benefits, enhance biodiversity, and are found in multiple configurations and assemblages across different climate and disturbance regimes. Biocrusts have been a focus of many ecologists, especially those working in semiarid and arid lands, as biocrusts are foundational community members, play fundamental roles in ecosystem processes, and offer rare opportunities to study biological interactions at small and large spatial scales. Due to these same characteristics, biocrusts have the potential to serve as an excellent teaching tool. The purpose of this paper is to demonstrate the utility of biocrust communities as a model system in science education. Functioning as portable, dynamic mini ecosystems, biocrusts can be used to teach about organisms, biodiversity, biotic interactions, abiotic controls, ecosystem processes, and even global change, and can be easy to use in nearly every classroom setup. For example, education principles, such as evolution and adaptation to stress, or structure and function (patterns and processes) can be applied by bringing biocrusts into the classroom as a teaching tool. In addition, discussing the utility of biocrusts in the classroom – including theory, hypothesis testing, experimentation, and hands-on learning – this document also provides tips and resources for developing education tools and activities geared toward impactful learning.

Frontiers in Microbiology