RESUMO
Deep-sea hydrothermal vents are important in global biogeochemical cycles, providing biological oases at the sea floor that are supported by the thermal and chemical flux from the Earth's interior. As hot, acidic and reduced hydrothermal fluids mix with cold, alkaline and oxygenated sea water, minerals precipitate to form porous sulphide-sulphate deposits. These structures provide microhabitats for a diversity of prokaryotes that exploit the geochemical and physical gradients in this dynamic ecosystem. It has been proposed that fluid pH in the actively venting sulphide structures is generally low (pH < 4.5), yet no extreme thermoacidophile has been isolated from vent deposits. Culture-independent surveys based on ribosomal RNA genes from deep-sea hydrothermal deposits have identified a widespread euryarchaeotal lineage, DHVE2 (deep-sea hydrothermal vent euryarchaeotic 2). Despite the ubiquity and apparent deep-sea endemism of DHVE2, cultivation of this group has been unsuccessful and thus its metabolism remains a mystery. Here we report the isolation and cultivation of a member of the DHVE2 group, which is an obligate thermoacidophilic sulphur- or iron-reducing heterotroph capable of growing from pH 3.3 to 5.8 and between 55 and 75 degrees C. In addition, we demonstrate that this isolate constitutes up to 15% of the archaeal population, providing evidence that thermoacidophiles may be key players in the sulphur and iron cycling at deep-sea vents.
Assuntos
Archaea/isolamento & purificação , Archaea/fisiologia , Temperatura Alta , Água do Mar , Ácidos , Archaea/classificação , Archaea/ultraestrutura , Fontes Termais , Concentração de Íons de Hidrogênio , Ferro/metabolismo , Dados de Sequência Molecular , Oceanos e Mares , Filogenia , RNA Ribossômico 16S/análise , RNA Ribossômico 16S/genética , Enxofre/metabolismoRESUMO
To evaluate the effects of local fluid geochemistry on microbial communities associated with active hydrothermal vent deposits, we examined the archaeal and bacterial communities of 12 samples collected from two very different vent fields: the basalt-hosted Lucky Strike (37°17'N, 32°16.3'W, depth 1600-1750 m) and the ultramafic-hosted Rainbow (36°13'N, 33°54.1'W, depth 2270-2330 m) vent fields along the Mid-Atlantic Ridge (MAR). Using multiplexed barcoded pyrosequencing of the variable region 4 (V4) of the 16S rRNA genes, we show statistically significant differences between the archaeal and bacterial communities associated with the different vent fields. Quantitative polymerase chain reaction (qPCR) assays of the functional gene diagnostic for methanogenesis (mcrA), as well as geochemical modelling to predict pore fluid chemistries within the deposits, support the pyrosequencing observations. Collectively, these results show that the less reduced, hydrogen-poor fluids at Lucky Strike limit colonization by strict anaerobes such as methanogens, and allow for hyperthermophilic microaerophiles, like Aeropyrum. In contrast, the hydrogen-rich reducing vent fluids at the ultramafic-influenced Rainbow vent field support the prevalence of methanogens and other hydrogen-oxidizing thermophiles at this site. These results demonstrate that biogeographical patterns of hydrothermal vent microorganisms are shaped in part by large scale geological and geochemical processes.
Assuntos
Archaea/classificação , Bactérias/classificação , Biodiversidade , Fontes Hidrotermais/microbiologia , Archaea/genética , Bactérias/genética , Sedimentos Geológicos/química , Sedimentos Geológicos/microbiologia , Geologia , Fontes Hidrotermais/química , Dados de Sequência Molecular , Filogenia , Reação em Cadeia da Polimerase , RNA Ribossômico 16S/genética , Água do Mar/química , Água do Mar/microbiologiaRESUMO
The fungal pathogen Batrachochytrium dendrobatidis (Bd) causes chytridiomycosis, a disease implicated in amphibian declines on 5 continents. Polymerase chain reaction (PCR) primer sets exist with which amphibians can be tested for this disease, and advances in sampling techniques allow non-invasive testing of animals. We developed filtering and PCR based quantitative methods by modifying existing PCR assays to detect Bd DNA in water and sediments, without the need for testing amphibians; we tested the methods at 4 field sites. The SYBR based assay using Boyle primers (SYBR/Boyle assay) and the Taqman based assay using Wood primers performed similarly with samples generated in the laboratory (Bd spiked filters), but the SYBR/Boyle assay detected Bd DNA in more field samples. We detected Bd DNA in water from 3 of 4 sites tested, including one pond historically negative for chytridiomycosis. Zoospore equivalents in sampled water ranged from 19 to 454 1(-1) (nominal detection limit is 10 DNA copies, or about 0.06 zoospore). We did not detect DNA of Bd from sediments collected at any sites. Our filtering and amplification methods provide a new tool to investigate critical aspects of Bd in the environment.
Assuntos
Quitridiomicetos/genética , Quitridiomicetos/isolamento & purificação , DNA Fúngico/análise , DNA Fúngico/genética , Microbiologia Ambiental , Água Doce/microbiologia , Sedimentos Geológicos/microbiologia , Doenças dos Animais/microbiologia , Animais , Dermatomicoses/veterinária , Reação em Cadeia da Polimerase , Sensibilidade e EspecificidadeRESUMO
This study examines the use of fecal indicator bacteria (FIB) as a predictor of the presence of Helicobacter spp. A combination of standard culture and molecular techniques were used to detect and quantify FIB, Helicobacter spp. and H. pylori from five North American rivers of different size and with different land use characteristics. Primers designed to amplify genes specific to Helicobacter spp. and H. pylori were evaluated for their efficacy in detection and quantification in environmental samples. Helicobacter spp. were detected in 18/33 (55%) of river samples. H. pylori was detected in 11/33 (33%) of river samples. FIB were found in 32/33 (96%) of river samples. When FIB abundance exceeded USEPA water quality standards for single samples, Helicobacter or H. pylori were detected in 7/15 (47%) cases. No numerical correlation was found between the presence of FIB and either Helicobacter spp. or H. pylori. This suggests that the presence of FIB will be of limited use for detection of Helicobacter spp. or H. pylori by public health agencies.
Assuntos
Fezes/microbiologia , Água Doce/microbiologia , Helicobacter pylori/isolamento & purificação , Rios/microbiologia , Microbiologia da Água , América do Norte , Reação em Cadeia da PolimeraseRESUMO
An in situ bioaugmentation (BA) experiment was conducted to understand processes controlling microbial dechlorination of trichloroethene (TCE) in groundwater at the Naval Air Warfare Center (NAWC), West Trenton, NJ. In the BA experiment, an electron donor (emulsified vegetable oil and sodium lactate) and a chloro-respiring microbial consortium were injected into a well in fractured mudstone of Triassic age. Water enriched in ²H was also injected as a tracer of the BA solution, to monitor advective transport processes. The changes in concentration and the δ¹³C of TCE, cis-dichloroethene (cis-DCE), and vinyl chloride (VC); the δ²H of water; changes in the abundance of the microbial communities; and the concentration of dissolved H2 gas compared to pre- test conditions, provided multiple lines of evidence that enhanced biodegradation occurred in the injection well and in two downgradient wells. For those wells where the biodegradation was stimulated intensively, the sum of the molar chlorinated ethene (CE) concentrations in post-BA water was higher than that of the sum of the pre-BA background molar CE concentrations. The concentration ratios of TCE/(cis-DCE+VC) indicated that the increase in molar CE concentration may result from additional TCE mobilized from the rock matrix in response to the oil injection or due to desorption/diffusion. The stable carbon isotope mass-balance calculations show that the weighted average ¹³C isotope of the CEs was enriched for around a year compared to the background value in a two year monitoring period, an effective indication that dechlorination of VC was occurring. Insights gained from this study can be applied to efforts to use BA in other fractured rock systems. The study demonstrates that a BA approach can substantially enhance in situ bioremediation not only in fractures connected to the injection well, but also in the rock matrix around the well due to processes such as diffusion and desorption. Because the effect of the BA was intensive only in wells where an amendment was distributed during injection, it is necessary to adequately distribute the amendments throughout the fractured rock to achieve substantial bioremediation. The slowdown in BA effect after a year is due to some extend to the decrease abundant of appropriate microbes, but more likely the decreased concentration of electron donor.
Assuntos
Poluentes Ambientais/metabolismo , Tricloroetileno/metabolismo , Biodegradação Ambiental , Biomassa , Isótopos de Carbono , Deutério/análise , Poluentes Ambientais/análise , Poluentes Ambientais/química , Água Subterrânea/química , Água Subterrânea/microbiologia , New Jersey , Tricloroetileno/análise , Tricloroetileno/químicaRESUMO
Although a large fraction of the world's biomass resides in the subsurface, there has been no study of the effects of catastrophic disturbance on the deep biosphere and the rate of its subsequent recovery. We carried out an investigation of the microbiology of a 1.76 km drill core obtained from the â¼35 million-year-old Chesapeake Bay impact structure, USA, with robust contamination control. Microbial enumerations displayed a logarithmic downward decline, but the different gradient, when compared to previously studied sites, and the scatter of the data are consistent with a microbiota influenced by the geological disturbances caused by the impact. Microbial abundance is low in buried crater-fill, ocean-resurge, and avalanche deposits despite the presence of redox couples for growth. Coupled with the low hydraulic conductivity, the data suggest the microbial community has not yet recovered from the impact â¼35 million years ago. Microbial enumerations, molecular analysis of microbial enrichment cultures, and geochemical analysis showed recolonization of a deep region of impact-fractured rock that was heated to above the upper temperature limit for life at the time of impact. These results show how, by fracturing subsurface rocks, impacts can extend the depth of the biosphere. This phenomenon would have provided deep refugia for life on the more heavily bombarded early Earth, and it shows that the deeply fractured regions of impact craters are promising targets to study the past and present habitability of Mars.
Assuntos
Geologia , Microbiologia do Solo , Bactérias/genética , Bactérias/isolamento & purificação , Baías/microbiologia , Genes Bacterianos/genética , Geografia , Hibridização in Situ Fluorescente , Dados de Sequência Molecular , Oxirredução , Análise de Regressão , Propriedades de Superfície , Virginia , Difração de Raios XRESUMO
High resolution direct-push profiling over short vertical distances was used to investigate CH(4) attenuation in a petroleum contaminated aquifer near Bemidji, Minnesota. The contaminant plume was delineated using dissolved gases, redox sensitive components, major ions, carbon isotope ratios in CH(4) and CO(2), and the presence of methanotrophic bacteria. Sharp redox gradients were observed near the water table. Shifts in δ(13)C(CH4) from an average of -57.6 (±1.7) in the methanogenic zone to -39.6 (±8.7) at 105m downgradient, strongly suggest CH(4) attenuation through microbially mediated degradation. In the downgradient zone the aerobic/anaerobic transition is up to 0.5m below the water table suggesting that transport of O(2) across the water table is leading to aerobic degradation of CH(4) at this interface. Dissolved N(2) concentrations that exceeded those expected for water in equilibrium with the atmosphere indicated bubble entrapment followed by preferential stripping of O(2) through aerobic degradation of CH(4) or other hydrocarbons. Multivariate and cluster analysis were used to distinguish between areas of significant bubble entrapment and areas where other processes such as the infiltration of O(2) rich recharge water were important O(2) transport mechanisms.
Assuntos
Monitoramento Ambiental/métodos , Metano/metabolismo , Methylococcaceae/metabolismo , Petróleo/metabolismo , Poluentes Químicos da Água/metabolismo , Aerobiose , Anaerobiose , Análise por Conglomerados , DNA/análise , DNA/isolamento & purificação , Monitoramento Ambiental/instrumentação , Gases/análise , Gases/química , Água Subterrânea/análise , Água Subterrânea/química , Água Subterrânea/microbiologia , Metano/análise , Metano/química , Minnesota , Análise Multivariada , Oxirredução , Oxigênio/análise , Oxigênio/química , Oxigênio/metabolismo , Petróleo/análise , Petróleo/microbiologia , Poluição por Petróleo/análise , Reação em Cadeia da Polimerase , Poluentes Químicos da Água/análise , Poluentes Químicos da Água/químicaRESUMO
Knowledge of the environmental constraints on a pathogen is critical to predicting its dynamics and effects on populations. Batrachochytrium dendrobatidis (Bd), an aquatic fungus that has been linked with widespread amphibian declines, is ubiquitous in the Rocky Mountains. As part of assessing the distribution limits of Bd in our study area, we sampled the water column and sediments for Bd zoospores in 30 high-elevation water bodies that lacked amphibians. All water bodies were in areas where Bd has been documented from neighboring, lower-elevation areas. We targeted areas lacking amphibians because existence of Bd independent of amphibians would have both ecologic and management implications. We did not detect Bd, which supports the hypothesis that it does not live independently of amphibians. However, assuming a detection sensitivity of 59.5% (based on sampling of water where amphibians tested positive for Bd), we only had 95% confidence of detecting Bd if it was in > or =16% of our sites. Further investigation into potential abiotic reservoirs is needed, but our results provide a strategic step in determining the distributional and environmental limitations of Bd in our study region.
Assuntos
Anfíbios/microbiologia , Quitridiomicetos/isolamento & purificação , Sedimentos Geológicos/microbiologia , Microbiologia da Água , Animais , Reservatórios de Doenças/microbiologia , Microbiologia Ambiental , Monitoramento Ambiental , Água Doce/microbiologia , Estados UnidosRESUMO
The relationship between environmental factors and functional gene diversity of ammonia-oxidizing bacteria (AOB) was investigated across a transect from the freshwater portions of the Chesapeake Bay and Choptank River out into the Sargasso Sea. Oligonucleotide probes (70-bp) designed to represent the diversity of ammonia monooxygenase (amoA) genes from Chesapeake Bay clone libraries and cultivated AOB were used to construct a glass slide microarray. Hybridization patterns among the probes in 14 samples along the transect showed clear variations in amoA community composition. Probes representing uncultivated members of the Nitrosospira-like AOB dominated the probe signal, especially in the more marine samples. Of the cultivated species, only Nitrosospira briensis was detected at appreciable levels. Discrimination analysis of hybridization signals detected two guilds. Guild 1 was dominated by the marine Nitrosospira-like probe signal, and Guild 2's largest contribution was from upper bay (freshwater) sediment probes. Principal components analysis showed that Guild 1 was positively correlated with salinity, temperature and chlorophyll a concentration, while Guild 2 was positively correlated with concentrations of oxygen, dissolved organic carbon, and particulate nitrogen and carbon, suggesting that different amoA sequences represent organisms that occupy different ecological niches within the estuarine/marine environment. The trend from most diversity of AOB in the upper estuary towards dominance of a single type in the polyhaline region of the Bay is consistent with the declining importance of AOB with increasing salinity, and with the idea that AO-Archaea are the more important ammonia oxidizers in the ocean.