Structural and Geomicrobiological Characteristics of a Microbial Community from a Cold Sulfide Spring

The Ancaster sulfur spring is a cold (9°C) sulfur spring located near Ancaster, Ontario, Canada, which hosts an abundant and diverse microbial mat community. We conducted an extensive microscopical study of the microbial community of this spring using a number of techniques: phase light, confocal scanning laser microscopy, conventional scanning electron microscopy using both chemical/critical point drying and cryofixation preparative techniques, environmental scanning electron microscopy, and transmission electron microscopy. The latter two techniques were coupled with energy dispersive X-ray spectrometry for elemental analysis to complement wet geochemical data collected on bulk spring water and mat pore water. In the anoxic source of the spring, green and purple sulfur bacteria were found together with a sulfide-utilizing type of cyanobacteria that had the unusual characteristic of storing colloidal sulfur intracellularly. Deeper within the source, the mats were dominated by green sulfur bacteria and thick biofilms of cells that precipitated Fe and Zn sulfide minerals on their surfaces. Downstream from the source, thick, filamentous white mats lined the stream channel, formed by a diverse mass of nonphotosynthetic sulfur oxidizers, which were responsible for forming thick masses of spherical colloidal sulfur. These were distinguished by ESEM-EDS from cells by their simple elemental composition (only S was detected). Aqueous geochemistry analysis by ICP-MS showed that some elements (Fe, C, P, Zn, Mg, Ba) were present at higher levels in mat pore water than in bulk spring water. Our approach allowed us to gain an appreciation of the characteristics of this microbial community and allowed us to develop a good understanding of the types of microorganisms present and infer some of the relationships among the members of the community. In addition, we wish to convey the utility of a thorough microscopical approach in geomicrobiological and microbial ecology studies.     

Five-Year Monitoring of Bacterial Communities in Dripping Water from the Heshang Cave in Central China: Implication for Paleoclimate Reconstruction and Ecological Functions

Microbial lipids in stalagmites are increasingly used to reconstruct the paleoclimate change, necessitating the investigations on microbial communities in dripping waters. A pilot molecular survey was conducted on bacterial communities of dripping waters at two sites (1D and 3D) in Heshang Cave of Hubei Province in central China for a period of 2008 to 2013. The samples were subjected to genome DNA extraction, 16S rRNA gene amplification, clone library construction and phylogenetic analysis to explore the seasonal variation of bacterial communities and their association with environmental factors including regional air temperature, precipitation, cave temperature, pH, conductivity and dripping rate of the water samples. Seasonal variations were clearly observed in components and diversities of bacterial communities at both sites. Bacterial community was dominated by Gammaproteobacteria in autumn and winter, whereas Betaproteobacteria became dominant in samples collected in summer and spring. Among the environmental factors investigated, regional air temperature was found to have a strong impact on bacterial communities indicated by cluster and redundancy analysis. Moreover the bacterial biodiversity was observed to increase with the temperature rising. Bacteria identified in dripping water were either oligotrophs or able to acquire nutrients from minerals under oligotrophic conditions. They may also be able to induce calcite precipitation in cave systems. Our data shed light on the potential of microbes used as a tool for the reconstruction of paleo-temperature as well as on the ecological functions of bacterial communities in oligotrophic caves.     

Metabolic Characterization of cold active Pseudomonas, Arthrobacter, Bacillus, and Flavobacterium spp. from Western Himalayas

Himalayan soils undergo dramatic temporal changes in their microclimatic properties. The soil habitats in the high altitude cold habitats of Himalayas are little explored with respect to bacterial diversity and metabolic potentials of the bacterial species. Soil habitat in Western Himalayas is dominated by the genera of Pseudomonas, Arthrobacter, Bacillus, and Flavobacterium. Strains were found to be diverse in their metabolic potentials to utilize different carbon sources by growing them on media containing 114 different sole carbon sources. Bacillus sp. STL9 was supported by the lowest number (12.3%) of the carbon sources while growth was observed in 73.7% of the carbon sources tested for the Pseudomonas sp. SPS2. Carbohydrates appeared to be preferred carbon sources for these Himalayan isolates followed by amino acids and proteins. These microbes also produced various extra-cellular hydrolytic enzymes having biotechnological potentials, lipase being the one secreted by most strains (85.7%) followed by β-galactosidase (42.8%). Antibiotic resistance profiling for 85 different antibiotics has also been described.     

Establishment of Microbial Eukaryotic Enrichment Cultures from a Chemically Stratified Antarctic Lake and Assessment of Carbon Fixation Potential

Lake Bonney is one of numerous permanently ice-covered lakes located in the McMurdo Dry Valleys, Antarctica. The perennial ice cover maintains a chemically stratified water column and unlike other inland bodies of water, largely prevents external input of carbon and nutrients from streams. Biota are exposed to numerous environmental stresses, including year-round severe nutrient deficiency, low temperatures, extreme shade, hypersalinity, and 24-hour darkness during the winter ¹. These extreme environmental conditions limit the biota in Lake Bonney almost exclusively to microorganisms ².Single-celled microbial eukaryotes (called "protists") are important players in global biogeochemical cycling ³ and play important ecological roles in the cycling of carbon in the dry valley lakes, occupying both primary and tertiary roles in the aquatic food web. In the dry valley aquatic food web, protists that fix inorganic carbon (autotrophy) are the major producers of organic carbon for organotrophic organisms ^{4, 2}. Phagotrophic or heterotrophic protists capable of ingesting bacteria and smaller protists act as the top predators in the food web ⁵. Last, an unknown proportion of the protist population is capable of combined mixotrophic metabolism ^{6, 7}. Mixotrophy in protists involves the ability to combine photosynthetic capability with phagotrophic ingestion of prey microorganisms. This form of mixotrophy differs from mixotrophic metabolism in bacterial species, which generally involves uptake dissolved carbon molecules. There are currently very few protist isolates from permanently ice-capped polar lakes, and studies of protist diversity and ecology in this extreme environment have been limited ^{8, 4, 9, 10, 5}. A better understanding of protist metabolic versatility in the simple dry valley lake food web will aid in the development of models for the role of protists in the global carbon cycle.We employed an enrichment culture approach to isolate potentially phototrophic and mixotrophic protists from Lake Bonney. Sampling depths in the water column were chosen based on the location of primary production maxima and protist phylogenetic diversity ^{4, 11}, as well as variability in major abiotic factors affecting protist trophic modes: shallow sampling depths are limited for major nutrients, while deeper sampling depths are limited by light availability. In addition, lake water samples were supplemented with multiple types of growth media to promote the growth of a variety of phototrophic organisms.RubisCO catalyzes the rate limiting step in the Calvin Benson Bassham (CBB) cycle, the major pathway by which autotrophic organisms fix inorganic carbon and provide organic carbon for higher trophic levels in aquatic and terrestrial food webs ¹². In this study, we applied a radioisotope assay modified for filtered samples ¹³ to monitor maximum carboxylase activity as a proxy for carbon fixation potential and metabolic versatility in the Lake Bonney enrichment cultures.     

Composition and Structure of Microbial Communities from Stromatolites of Hamelin Pool in Shark Bay, Western Australia

Stromatolites, organosedimentary structures formed by microbial activity, are found throughout the geological record and are important markers of biological history. More conspicuous in the past, stromatolites occur today in a few shallow marine environments, including Hamelin Pool in Shark Bay, Western Australia. Hamelin Pool stromatolites often have been considered contemporary analogs to ancient stromatolites, yet little is known about the microbial communities that build them. We used DNA-based molecular phylogenetic methods that do not require cultivation to study the microbial diversity of an irregular stromatolite and of the surface and interior of a domal stromatolite. To identify the constituents of the stromatolite communities, small subunit rRNA genes were amplified by PCR from community genomic DNA with universal primers, cloned, sequenced, and compared to known rRNA genes. The communities were highly diverse and novel. The average sequence identity of Hamelin Pool sequences compared to the >200,000 known rRNA sequences was only ~92%. Clone libraries were ~90% bacterial and ~10% archaeal, and eucaryotic rRNA genes were not detected in the libraries. The most abundant sequences were representative of novel proteobacteria (~28%), planctomycetes (~17%), and actinobacteria (~14%). Sequences representative of cyanobacteria, long considered to dominate these communities, comprised <5% of clones. Approximately 10% of the sequences were most closely related to those of α-proteobacterial anoxygenic phototrophs. These results provide a framework for understanding the kinds of organisms that build contemporary stromatolites, their ecology, and their relevance to stromatolites preserved in the geological record.     

Diversity,Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland

Various types of cyanobacterial mats were predominant in a wetland, constructed for the remediation of oil-polluted residual waters from an oil field in the desert of the south-eastern Arabian Peninsula, although such mats were rarely found in other wetland systems. There is scarce information on the bacterial diversity, spatial distribution and oil-biodegradation capabilities of freshwater wetland oil-polluted mats. Microbial community analysis by Automated Ribosomal Spacer Analysis (ARISA) showed that the different mats hosted distinct microbial communities. Average numbers of operational taxonomic units (OTUs_ARISA) were relatively lower in the mats with higher oil levels and the number of shared OTUs_ARISA between the mats was <60% in most cases. Multivariate analyses of fingerprinting profiles indicated that the bacterial communities in the wetland mats were influenced by oil and ammonia levels, but to a lesser extent by plant density. In addition to oil and ammonia, redundancy analysis (RDA) showed also a significant contribution of temperature, dissolved oxygen and sulfate concentration to the variations of the mats’ microbial communities. Pyrosequencing yielded 282,706 reads with >90% of the sequences affiliated to Proteobacteria (41% of total sequences), Cyanobacteria (31%), Bacteriodetes (11.5%), Planctomycetes (7%) and Chloroflexi (3%). Known autotrophic (e.g. Rivularia) and heterotrophic (e.g. Azospira) nitrogen-fixing bacteria as well as purple sulfur and non-sulfur bacteria were frequently encountered in all mats. On the other hand, sequences of known sulfate-reducing bacteria (SRBs) were rarely found, indicating that SRBs in the wetland mats probably belong to yet-undescribed novel species. The wetland mats were able to degrade 53–100% of C₁₂–C₃₀ alkanes after 6 weeks of incubation under aerobic conditions. We conclude that oil and ammonia concentrations are the major key players in determining the spatial distribution of the wetland mats’ microbial communities and that these mats contribute directly to the removal of hydrocarbons from oil field wastewaters.     

Peptidase Activity of Proteinivorax Bacteria and Their Possible Ecological Role in the Microbial Communities of Tanatar Soda Lakes (Altai Krai,Russia)

Microbiology - Peptidase activity of alkaliphilic anaerobic proteolytic Proteinivorax bacteria, P. tanatarense Z-910T and P. hydrogeniformans Z-710T, isolated from the Tanatar system of hypersaline...     

Microbial and Geochemical Assessment of Bauxitic Un-mined and Post-mined Chronosequence Soils from Mocho Mountains, Jamaica

Microorganisms are very sensitive to environmental change and can be used to gauge anthropogenic impacts and even predict restoration success of degraded environments. Here, we report assessment of bauxite mining activities on soil biogeochemistry and microbial community structure using un-mined and three post-mined sites in Jamaica. The post-mined soils represent a chronosequence, undergoing restoration since 1987, 1997, and 2007. Soils were collected during dry and wet seasons and analyzed for pH, organic matter (OM), total carbon (TC), nitrogen (TN), and phosphorus. The microbial community structure was assessed through quantitative PCR and massively parallel bacterial ribosomal RNA (rRNA) gene sequencing. Edaphic factors and microbial community composition were analyzed using multivariate statistical approaches and revealed a significant, negative impact of mining on soil that persisted even after greater than 20?years of restoration. Seasonal fluctuations contributed to variation in measured soil properties and community composition, but they were minor in comparison to long-term effects of mining. In both seasons, post-mined soils were higher in pH but OM, TC, and TN decreased. Bacterial rRNA gene analyses demonstrated a general decrease in diversity in post-mined soils and up to a 3-log decrease in rRNA gene abundance. Community composition analyses demonstrated that bacteria from the Proteobacteria (α, β, γ, δ), Acidobacteria, and Firmicutes were abundant in all soils. The abundance of Firmicutes was elevated in newer post-mined soils relative to the un-mined soil, and this contrasted a decrease, relative to un-mined soils, in proteobacterial and acidobacterial rRNA gene abundances. Our study indicates long-lasting impacts of mining activities to soil biogeochemical and microbial properties with impending loss in soil productivity.     

Effects of Copper,Nickel, and Sulfate from the Smelters at Sudbury,Ontario (Canada) on Microbial Communities in Lakes

Analysis of water and sediments from deep and shallow environments in lakes located 6–154 km east or southeast of the smelters at Sudbury, Ontario (Canada) revealed variable, interactive effects of copper, nickel, and sulfate from smelter fallout on lacustrine microfloras. Metal species in sediments were differentiated by sequential extractions, and the nature, abundances, and activities of microbial populations were represented by chlorophyll-a in water and by CO₂ production, fatty acids, phospholipids, dehydrogenase, alkaline phosphatase, and spectral properties of humic matter in sediments. Smelter fallout declined logarithmically with distance from the smelters, and its effects on microfloras depended on the type of microorganism or microbial process and on environmental factors and the abundances of metal species and detoxifying agents. Extractable copper and nickel had toxic effects, which were not attributable solely to the exchangeable fractions, but in certain cases nickel counteracted copper toxicity. Sedimentary sulfide as a whole or sulfide produced by bacterial sulfate reduction, or low oxidation–reduction potential regardless of sulfide concentration, ameliorated metal toxicity by making the metals less bioavailable; and toxicity showed a “quantum jump” when detoxifying agents fell below certain critical concentrations, implying the existence of threshold levels of bioavailable metals above which toxicity increased abruptly. In some cases metal toxicity was lowest in the lakes closest to the smelters (because sulfate concentrations were highest) as well as in the lakes furthest away, and was highest at intermediate distances. The results also suggest that nickel pollution led to ecological succession whereby nickel-tolerant microbial populations replaced nickel-sensitive ones.     

Patterns in the Composition of Microbial Communities from a Subtropical River: Effects of Environmental,Spatial and Temporal Factors

Microbes are key components of aquatic ecosystems and play crucial roles in global biogeochemical cycles. However, the spatiotemporal dynamics of planktonic microbial community composition in riverine ecosystems are still poorly understood. In this study, we used denaturing gradient gel electrophoresis of PCR-amplified 16S and 18S rRNA gene fragments and multivariate statistical methods to explore the spatiotemporal patterns and driving factors of planktonic bacterial and microbial eukaryotic communities in the subtropical Jiulong River, southeast China. Both bacterial and microbial eukaryotic communities varied significantly in time and were spatially structured according to upper stream, middle-lower stream and estuary. Among all the environmental factors measured, water temperature, conductivity, PO₄-P and TN/TP were best related to the spatiotemporal distribution of bacterial community, while water temperature, conductivity, NO_x-N and transparency were closest related to the variation of eukaryotic community. Variation partitioning, based on partial RDA, revealed that environmental factors played the most important roles in structuring the microbial assemblages by explaining 11.3% of bacterial variation and 17.5% of eukaryotic variation. However, pure spatial factors (6.5% for bacteria and 9.6% for eukaryotes) and temporal factors (3.3% for bacteria and 5.5% for eukaryotes) also explained some variation in microbial distribution, thus inherent spatial and temporal variation of microbial assemblages should be considered when assessing the impact of environmental factors on microbial communities.     

Phospholipid Fatty Acid Composition, Biomass, and Activity of Microbial Communities from Two Soil Types Experimentally Exposed to Different Heavy Metals

The phospholipid fatty acid (PLFA) pattern was analyzed in a forest humus and in an arable soil experimentally polluted with Cd, Cu, Ni, Pb, or Zn at different concentrations. In both soil types, there were gradual changes in the PLFA patterns for the different levels of metal contamination. The changes in the forest soil were similar irrespective of which metal was used, while in the arable soil the changes due to Cu contamination differed from those due to the other metals. Several PLFAs reacted similarly to the metal amendments in the two soil types, while others showed different responses. In both soils, the metal pollution resulted in a decrease in the iso-branched PLFAs i15:0 and i17:0 and in the monounsaturated 16:1ω5 and 16:1ω7c fatty acids, while increases were found for i16:0, the branched br17:0 and br18:0, and the cyclopropane cy17:0 fatty acids. In the forest soil, the methyl branched PLFAs 10Me16:0, 10Me17:0, and 10Me18:0 increased in metal-polluted soils, indicating an increase in actinomycetes, while in the arable soil a decrease was found for 10Me16:0 and 10Me18:0 in response to most metals. The bacterial PLFAs 15:0 and 17:0 increased in all metal-contaminated samples in the arable soil, while they were unaffected in the forest soil. Fatty acid 18:2ω6, which is considered to be predominantly of fungal origin, increased in the arable soil, except in the Cu-amended samples, in which it decreased instead. Effects on the PLFA patterns were found at levels of metal contamination similar to or lower than those at which effects on ATP content, soil respiration, or total amount of PLFAs had occurred.     

Organophosphate Pesticide Residues in Drinking Water from Artesian Wells and Health Risk Assessment of Agricultural Communities,Thailand

Organophosphate pesticide (OPPs) concentrations in artesian wells located in Thai agricultural and non-agricultural communities were studied during both wet and dry seasons. A total of 100 water samples were collected and subjects were asked to complete a survey. Gas chromatography flame photometric detector was used for OPP analysis. The average OPP concentration in the agricultural communities (0.085 and 0.418 μg/l in dry and wet season) was higher than in the non-agricultural communities (0.004 μg/l in both seasons). Ingestion of OPPs in contaminated water in the agricultural communities were estimated to be 0.187 and 0.919 μg/day during the dry and wet seasons, respectively, and 0.008 μg/day during both seasons in the non-agricultural communities. Agricultural communities were exposed to pesticide residues under the oral chronic reference dose. This study suggests that people in agricultural communities may be exposed to significantly greater levels of pesticides than non-agricultural populations during the dry and wet seasons (p < .001, .001).     

Ecological Risks Assessment and Pollution Source Identification of Trace Elements in Contaminated Sediments from the Pearl River Delta, China

Sediments from 14 stations in the Foshan Waterway, a river crossing the industrial district of Guangdong Province, South China, were sampled and subsequently analyzed. The 14 stations were selected for the pollution discharging features of the river, such as the hydrology, the distribution of pollution sources, and the locations of wastewater outlets. The ecological risks were assessed, and the pollution sources were identified to provide valuable information for environmental impact assessment and pollution control. The spatial variability was high and the range were (in milligrams per kilogram dry weight): Pb, 46.0~382.8; Cu, 33.7~ 482.3; Zn, 62.2~1,568.7; Ni, 28.5~130.7; Cr, 34.7~1,656.1; Cd, 0.50~8.53; Hg, 0.02~8.27; and As, 5.77~66.09. The evaluation results of enrichment factor and potential ecological risk index indicate that the metal pollution in the surface and bottom sediments were severely polluted and could pose serious threat to the ecosystem in most stations. Although the hazard levels of the trace element differed among the stations, Hg was the most serious pollutant in all stations. The results of principal component analysis (PCA) show that the discharge of industrial wastewater is the most important polluting factor whereas domestic sewage, which contains a large amount of organic substances, accelerates metal deposition. And potential pollution sources were identified by the way of integrating the analysis results of PCA and data gained from the local government. Therefore, the conclusion is drawn that Foshan Waterway is seriously polluted with trace elements, both in the surface sediment (0 to 20 cm) and the bottom sediments (21 to 50 cm) are contaminated.     

Ecological Risk Assessment of Arsenic and Metals in Surface Sediments from Estuarine and Coastal Areas of the Southern Bohai Sea,China

Distribution and magnitude of arsenic and metals in surface sediments collected from the coastal and estuarine areas of the southern Bohai Sea, China, were investigated. Sediments from the estuarine and coastal areas of the Jie and Xiaoqing Rivers contained highest concentrations of arsenic, cadmium, copper, mercury, and zinc. Mean concentrations of Cu, Zn, Cr, Pb, and Cd were higher than background concentrations determined for the areas. The magnitude of both enrichment factors (EF) and geoaccumulation indices (I_geo) suggested that pollution with As and metals was occurring along estuarine and coastal areas of the southern Bohai Sea. Risk analysis also suggested that concentrations of As and metals were sufficiently elevated as to cause adverse biological effects in the study area. According to the ecological risk index (RI) values, the upstream of the Jie River has a very high ecological risk for the waterbody. The data provided in this study are considered crucial for controlling and remediation of As and metals’ pollution of the southern Bohai Sea.     

Ca2+ and Mg2+-Stimulated ATPases from Roots of Plantago lanceolata, Plantago media and Plantago coronopus: Response to Alterations of the Level of Mineral Nutrition and Ecological Significance

Growth of Plantago lanceolata L., P. media L. and P. coronopus L. was followed at two levels of mineral nutrition (low-salt and high-salt). In addition the response of transfer of plants from low-salt conditions to high-salt conditions and vice versa was studied. Growth of these Plantago species was not much affected by the nutritional level. P. coronopus showed the least dependence on the level of mineral nutrition. The Ca²⁺- and Mg²⁺-stimulated ATPase activity of microsomal preparations of the roots of Plantago was also studied. A pH optimum at pH 6.5 was observed in all species, together with a relatively high ATPase activation by Mg²⁺ in P. lanceolata, by Ca²⁺ in P. media, and by both ions in P. coronopus. The specific activity of the ATPases was highest in preparations from low-salt roots. The three species all occur in relatively nutrient-poor habitats, but they are at the same time particularly adapted to circumneutral soils (P. lanceolata), to Ca²⁺-rich soils (P. media) and to alternating levels of mineral nutrition (P. coronopus). The properties of the ATPases (K_m, V_max, protein content) and the growth are discussed in relation to these ecological properties of the species.