The preservation and degradation of filamentous bacteria and biomolecules within iron oxide deposits at Rio Tinto, Spain

One of the keys to understanding and identifying life on other planets is to study the preservation of organic compounds and their precursor micro-organisms on Earth. Rio Tinto in southwestern Spain is a well documented site of microbial preservation within iron sulphates and iron oxides over a period of 2.1 Ma. This study has investigated the preservation of filamentous iron oxidising bacteria and organics through optical microscopy, scanning electron microscopy (SEM) and Fourier transform infra-red (FTIR) spectroscopy, from laboratory cultures of natural samples to contemporary natural materials to million-year old river terraces. Up to 40% elemental carbon and >7% nitrogen has been identified within microbial filaments and cell clusters in all samples through SEM EDS analyses. FTIR spectroscopy identified C-H(x) absorption bands between 2960 and 2800 cm(-1), Amide I and II absorption bands at 1656 and 1535 cm(-1), respectively and functional group vibrations from within nucleic acids at 917, 1016 and 1124 cm(-1). Absorption bands tracing the diagenetic transformation of jarosite to goethite to hematite through the samples are also identified. This combination of mineralogy, microbial morphology and biomolecular evidence allows us to further understand how organic fossils are created and preserved in iron-rich environments, and ultimately will aid in the search for the earliest life on Earth and potential organics on Mars.     

Methanogenesis in the sediments of Rio Tinto, an extreme acidic river

Río Tinto (Iberian Pyritic Belt, SW Spain) is well known for its low pH (mean pH 2.3), high redox potential (> +400 mV) and high concentration of heavy metals. In this work we describe and analyse the presence of methanogenic archaea in the extreme acidic and oxidizing environment of the Tinto basin. Methane formation was measured in microcosms inoculated with sediments from the Rio Tinto basin. Methanol, formate, volatile fatty acids and lactate stimulated the production of methane. Methane formation was associated with a decrease of redox potential and an increase in pH. Cores showed characteristic well-defined black bands in which a high acetate concentration was measured among the otherwise reddish-brown sediments with low acetate concentration. Methanosaeta concilii was detected in the black bands. In enrichment cultures, M. concilii (enriched with a complex substrate mixture), Methanobacterium bryantii (enriched with H(2)) and Methanosarcina barkeri (enriched with methanol) were identified. Our results suggest that methanogens thrive in micro-niches with mildly acidic and reducing conditions within Rio Tinto sediments, which are, in contrast, immersed in an otherwise extremely acidic and oxidizing environment.     

Phospholipid Fatty Acid Composition and Heavy Metal Tolerance of Soil Microbial Communities along Two Heavy Metal-Polluted Gradients in Coniferous Forests

The effects of long-term heavy metal deposition on microbial community structure and the level of bacterial community tolerance were studied along two different gradients in Scandinavian coniferous forest soils. One was near the Harjavalta smelter in Finland, and one was at Ronnskar in Sweden. Phospholipid fatty acid (PLFA) analysis revealed a gradual change in soil microbial communities along both pollution gradients, and most of the individual PLFAs changed similarly to metal pollution at both sites. The relative quantities of the PLFAs br18:0, br17:0, i16:0, and i16:1 increased with increasing heavy metal concentration, while those of 20:4 and 18:2(omega)6, which is a predominant PLFA in many fungi, decreased. The fungal part of the microbial biomass was found to be more sensitive to heavy metals. This resulted in a decreased fungal/bacterial biomass ratio along the pollution gradient towards the smelters. The thymidine incorporation technique was used to study the heavy metal tolerance of the bacteria. The bacterial community at the Harjavalta smelter, exposed mainly to Cu deposition, exhibited an increased tolerance to Cu but not to Cd, Ni, and Zn. At the Ronnskar smelter the deposition consisting of a mixture of metals increased the bacterial community tolerance to all tested metals. Both the PLFA pattern and the bacterial community tolerance were affected at lower soil metal concentrations than were bacterial counts and bacterial activities. At Harjavalta the increased Cu tolerance of the bacteria and the change in the PLFA pattern of the microbial community were found at the same soil Cu concentrations. This indicated that the altered PLFA pattern was at least partly due to an altered, more metal-tolerant bacterial community. At Ronnskar, where the PLFA data varied more, a correlation between bacterial community tolerance and an altered PLFA pattern was found up to 10 to 15 km from the smelter. Farther away changes in the PLFA pattern could not be explained by an increased community tolerance to metals.     

Macrofilamentous microbial communities in the metal-rich and acidic River Tinto, Spain

A novel type of macroscopic microbial community consisting of large dendritic filaments (up to 1.5 m) in a pH 2.0 dam of the River Tinto (South-western Spain) is described. The combined use of 16S rRNA-gene surveys and fluorescent in situ hybridisation (FISH) suggested that gamma-proteobacteria and a relative large diversity of alpha-proteobacteria dominated these structures. beta-Proteobacteria, Actinobacteria and Firmicutes were also detected. Whereas acidophilic bacteria of the genera Acidithiobacillus, Leptospirillum and Acidiphilium, and archaea belonging to the Thermoplasmatales dominate mine acid drainage waters and streamers (riverbed filamentous biofilms), none of the lineages identified in this study affiliate to typical acid mine drainage acidophilic bacteria. Bacteria of the Tinto macrofilaments might be heterotrophic, and could be feeding on the organic matter entrapped in the filamentous structure.     

Eukaryotic community distribution and its relationship to water physicochemical parameters in an extreme acidic environment, Rio Tinto (southwestern Spain)

The correlation between water physicochemical parameters and eukaryotic benthic composition was examined in Río Tinto. Principal component analysis showed a high inverse relationship between pH and most of the heavy metals analyzed as well as Dunaliella sp., while Chlamydomonas sp. abundance was positively related. Zn, Cu, and Ni clustered together and showed a strong inverse correlation with the diversity coefficient and most of the species analyzed. These eukaryotic communities seem to be more influenced by the presence of heavy metals than by the pH.     

Paleomobility in the Tiwanaku Diaspora: Biogeochemical analyses at Rio Muerto,Moquegua, Peru

Paleomobility has been a key element in the study of the expansion of ancient states and empires, including the Tiwanaku polity of the South Central Andes (AD 500–1000). We present radiogenic strontium and oxygen isotope data from human burials from three cemeteries in the Tiwanaku‐affiliated Middle Horizon archaeological site complex of Rio Muerto in the Moquegua Valley of southern Peru. At Rio Muerto, archaeological human enamel and bone values range from ⁸⁷Sr/⁸⁶Sr = 0.70657–0.72018, with a mean of ⁸⁷Sr/⁸⁶Sr = 0.70804 ± 0.00207 (1σ, n = 55). For the subset of samples analyzed for oxygen isotope values (n = 48), the data ranges from δ¹⁸O_{carbonate(VSMOW)} = +18.1 to +27.0‰. When contextualized with other lines of archaeological evidence, we interpret these data as evidence for an archaeological population in which the majority of individuals had “local” origins, and were likely second‐generation, or more, immigrants from the Tiwanaku heartland in the altiplano. Based on detailed life history data, we argue a smaller number of individuals came at different ages from various regions within the Tiwanaku polity. We consider whether these individuals with isotopic values consistent with “nonlocal” geographic origins could represent first‐generation migrants, marriage exchange partners, or occupationally mobile herders, traders or other travelers. By combining isotopic life history studies with mortuary treatment data, we use a person‐centered migration history approach to state integration and expansion. Isotopic analyses of paleomobility at the Rio Muerto site complex contribute to the role of diversity in ancient states by demonstrating the range of geographic origins rather than simply colonists from the Lake Titicaca Basin. Am J Phys Anthropol 155:405–421, 2014. © 2014 Wiley Periodicals, Inc.     

Response of Aquatic Hyphomycete Communities to Changes in Heavy Metal Exposure

Decomposition of Alnus glutinosa (alder) leaves was studied in a severely (site H4) and a moderately (site H8) heavy metal polluted stream in the former copper shale mining district of Mansfeld, Central Germany. Leaves at H8 had reduced fungal diversity and spore production but a high exponential decay rate (k = 0.065). No further mass loss of leaves occurred at H4 after 4–6 weeks, and fungal diversity and spore production were lower than in H8. Decay and sporulation rates gradually increased to values of H8 control leaves in leaves preincubated in H4 and then transferred to H8. These increases correlated with the invasion of transplanted leaves by Tetracladium marchalianum and Tricladium angulatum. In the reverse transplant experiment (H8 to H4), mass loss appeared to stop immediately. Sporulation rates also declined, but remained consistently above levels in H4 control leaves. Leaves precolonized in the laboratory by one of three aquatic hyphomycete species exhibited increased decay rates in both streams. Sporulation rates on these leaves were greater than those of control leaves in H4, but smaller than those of control leaves in H8. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Heavy Metal Distribution in Open Canals and Drains in the Upper Rio Grande Basin

The inclusion of reclaimed effluents for irrigated agriculture may allow communities along the U.S.-Mexico border to use water resources more efficiently and reduce urban costs of wastewater treatment. However, metal inflow from industry and urbanization may threaten food safety. This study examines metal concentrations in sediments from open canal systems charged with flow from the Rio Grande and from effluents discharged from border communities. At the surface of canal beds, sediments were collected from six canal segments that began at the fringe of the El Paso/Juarez metroplex to rural areas downstream, and ranged from 9 to 24?km in length. Sediments were analyzed for Cd, Co, Cr, Cu, Ni, Pb, and Zn. These metals rarely exceeded 20?mg kg^?1. Drainage and effluent conveyance increased the variability of metal concentrations in sediments. Geostatistical models did not significantly account for spatial variability of metals, except in Mexico. This may implicate multiple rather than single inflow sources of metals. Peaks in metal concentrations often coincided with growing rural communities. However, most metal concentrations were within conventional global ranges and were not at levels high enough to threaten food safety. Future sampling strategies will require reduced sampling intervals from 1 to <0.13?km.     

A Novel Family of Ubiquitous Heavy Metal Ion Transport Proteins

We describe a novel diverse family of metal ion transporter (CDF) proteins (the cation diffusion facilitator (CDF) family) with members occurring in both prokaryotes and eukaryotes. Thirteen sequenced protein members of the CDF family have been identified, several of which have been shown to transport cobalt, cadmium and/or zinc. All members of the CDF family possess six putative transmembrane spanners with strongest conservation in the four N-terminal spanners, and on the basis of the analyses, we present a unified structural model. Members of the family are shown to exhibit an unusual degree of size variation, sequence divergence, and differences in cell localization and polarity. The phylogenetic tree for the CDF family reveals that prokaryotic and eukaryotic proteins cluster separately. It allows functional predictions for some uncharacterized members of this family. A signature sequence specific for the CDF family is derived. Received: 15 July 1996/Revised: 21 October 1996     

Effect of Namomaterials on Heavy Metal Transport in Alkaline Soil

A high level of heavy metals in soil would negatively impact human health if these metals are consumed by humans through the food chain. The effect of nanomaterials, including SiO₂-Al₂O₃-Fe₂O₃, on heavy metals in alkaline soil was studied through simulating leaching in the soil column. Nanomaterials that weighed 4%, 6%, and 10% of the soil mass were added to a soil column in which garlic was planted. Leaching tests were conducted. Heavy metals in the soil leachate of different soil depths and different parts of the plant planted in the soil column were determined using a high-resolution inductively coupled plasma mass spectrometer (HR-ICP-MS). The results indicated that the migration of heavy metals through alkaline soil was inhibited. In the test with nanomaterials of 4% soil mass, 63% Cu, 79% Cd, 68% Pb, 89% Zn, and 76% Ni were decreased compared to the control. When the addition of nanomaterials was up to 6% of soil mass, 82% Cu, 92% Cd, 76% Pb, 91% Zn, and 88% Ni were reduced, respectively. No additional apparent results were observed with more nanomaterials added to the soil column. The nanomaterials effectively prevented heavy metal migration, especially inhibiting heavy metal migration downward. Nanomaterials will be promising in subsequent studies.     

Promising Biological Indicator of Heavy Metal Pollution: Bioluminescent Bacterial Strains Isolated and Characterized from Marine Niches of Goa,India

In present study, several marine water samples collected from the North Goa Beaches, India for isolation of luminescent bacterial species. Isolates obtained labelled as DP1-5 and AB1-6. Molecular characterization including identification of a microbial culture using 16S rRNA gene based molecular technique and phylogenetic analysis confirmed that DP3 & AB1 isolates were Vibrio harveyi. All of the isolates demonstrated multiple metal resistances in terms of growth, with altered luminescence with variable metal concentration. Present investigations were an attempt towards exploring and reporting an updated diversity of bioluminescent bacterial species from various sites around the Goa, India which would be explored in future for constructing luminescence based biosensor for efficiently monitoring the level of hazardous metals in the environment.

Electronic supplementary material

The online version of this article (doi:10.1007/s12088-015-0531-y) contains supplementary material, which is available to authorized users.     

Population Changes of Soil Microbial Communities Induced by Hydrocarbon and Heavy Metal Contamination

Substrate utilization tests with Biolog® plates were used to obtain information on shifts in community composition and on changes in the metabolic diversity and activity of microorganisms in soil polluted with hydrocarbons. and/or heavy metals. Differences between the patterns of substrate utilization of endogenous microorganisms of pristine and contaminated soils were investigated by multivariate analysis. Population changes and shifts in metabolic diversity were observed both after hydrocarbon pollution or heavy metal contamination. The overall activity on the 95 Biolog® Gram-negative (GN) substrates correlated well with the respiration rate of the soil. Soils contaminated with hydrocarbons showed higher metabolic potentials than the corresponding controls. In contrast, heavy metal pollution caused both lower metabolic activity and a loss in diversity. The Biolog® assay was found to be suitable to describe changes in functional diversity of soils caused by hydrocarbon contamination or heavy metal stress.     

Ecological study of the fungal populations of the acidic Tinto River in southwestern Spain

The characterization of the microbial ecology of the Tinto River, an extreme habitat with an extremely low pH and a high concentration of heavy metals, revealed an unexpected level of microbial richness. A variety of microbial eukaryotes was isolated, among them several fungal strains that were identified and their physiological characteristics studied. Ninety strains of yeast were isolated from the Tinto River. Fifty-two percent of them were capable of growth in vitro using medium amended with river water. They belong to 6 genera of basidiomycetes (Rhodotorula, Cryptococcus, Tremella, Holtermannia, Leucosporidium, and Mrakia) and 2 of ascomycetes (Candida and Williopsis). In addition, 349 strains of hyphomycetes belonging to 17 genera (most of them ascomycetes) were isolated and studied. Forty-four percent of the isolated filamentous fungi (154 strains) were capable of growing in vitro using medium amended with Tinto River water. Of this percentage, 19% (29 strains) belonged to the genus Penicillium (16 species) and 66% (102 strains) were included in the genera Scytalidium, Bahusakala, Phoma, and Heteroconium or showed dark sterile mycelia, which probably are of dematiaceous hyphomycetes. In addition, we characterized strains of the ascomycete genera Lecythophora and Acremonium and of the zygomycete genus Mortierella, all of them capable of growing in medium amended with river water. Statistical correlation of biological and physicochemical variables suggested a positive relationship between the dematiaceous hyphomycetes and the most extreme physicochemical conditions found in the Tinto River. Principal components analysis confirmed this relationship and also showed that the Acremonium and Lecythophora groups had environmental preferences similar to those of dematiaceous fungi. The spatial positions of the sampling sites were grouped in 2 main clusters: (i) sampling sites in the mine zone in which most of the dematiaceous, Acremonium, and Lecythophora strains were isolated and (ii) sites that were not in the mine zone and sampling station 5 from which were isolated mainly strains of fungi that were not capable of growing in the medium amended with river water and species of the Penicillium genus.     

Microbial Community Composition and Ecology of an Acidic Aquatic Environment: The Tinto River, Spain

We studied the correlation between physicochemical and biological characteristics of an acidic river, the Tinto River, in Southwestern Spain. The Tinto River is an extreme environment characterized by its low pH (mean of 2.2) and high concentrations of heavy metals (Fe 2.3 g/L, Zn 0.22 g/L, Cu 0.11 g/L). These extreme conditions are the product of the metabolic activity of chemolithotrophic microorganisms, including iron- and sulfur-oxidizing bacteria, that can be found in high concentrations in its waters. The food chain in the river is very constrained and exclusively microbial. Primary productivity in the Tinto River is the sum of photosynthetic and chemolithotrophic activity. Heterotrophic bacteria and fungi are the major decomposers and protists are the major predators. A correlation analysis including the physicochemical and biological variables suggested a close relationship between the acidic pH values and abundance of both chemolithotrophic bacteria and filamentous fungi. Chemolithotrophic bacteria correlated with the heavy metals found in the river. A principal component analysis of the biotic and abiotic variables suggested that the Tinto River ecosystem can be described as a function of three main groups of variables: pH values, metal concentrations, and biological productivity.     

Multiple Heavy Metal Tolerance of Soil Bacterial Communities and Its Measurement by a Thymidine Incorporation Technique

A thymidine incorporation technique was used to determine the tolerance of a soil bacterial community to Cu, Cd, Zn, Ni, and Pb. An agricultural soil was artificially contaminated in our laboratory with individual metals at three different concentrations, and the results were compared with the results obtained by using the plate count technique. Thymidine incorporation was found to be a simple and rapid method for measuring tolerance. Data obtained by this technique were very reproducible. A linear relationship was found between changes in community tolerance levels obtained by the thymidine incorporation and plate count techniques (r = 0.732, P < 0.001). An increase in tolerance to the metal added to soil was observed for the bacterial community obtained from each polluted soil compared with the community obtained from unpolluted soil. The only exception was when Pb was added; no indication of Pb tolerance was found. An increase in the tolerance to metals other than the metal originally added to soil was also observed, indicating that there was multiple heavy metal tolerance at the community level. Thus, Cu pollution, in addition to increasing tolerance to Cu, also induced tolerance to Zn, Cd, and Ni. Zn and Cd pollution increased community tolerance to all five metals. Ni amendment increased tolerance to Ni the most but also increased community tolerance to Zn and, to lesser degrees, increased community tolerance to Pb and Cd. In soils polluted with Pb increased tolerance to other metals was found in the following order: Ni > Cd > Zn > Cu. We found significant positive relationships between changes in Cd, Zn, and Pb tolerance and, to a lesser degree, between changes in Pb and Ni tolerance when all metals and amendment levels were compared. The magnitude of the increase in heavy metal tolerance was found to be linearly related to the logarithm of the metal concentration added to the soil. Threshold tolerance concentrations were estimated from these linear relationships, and changes in tolerance could be detected at levels of soil contamination similar to those reported previously to result in changes in the phospholipid fatty acid pattern (Å. Frostegård, A. Tunlid, and E. Bååth, Appl. Environ. Microbiol. 59: 3605-3617, 1993).     

The Structure and Biogeochemical Activity of the Phototrophic Communities from the Bol'sherechenskii Alkaline Hot Spring

Microbial communities growing in the bed of the alkaline, sulfide hot spring Bol'sherechenskii (the Baikal rift area) were studied over many years (1986–2001). The effluent water temperature ranged from 72 to 74°C, pH was from 9.25 to 9.8, and sulfide content was from 12 to 13.4 mg/ml. Simultaneous effects of several extreme factors restrict the spread of phototrophic microorganisms. Visible microbial mat appears with a decrease in the temperature to 62°C and in sulfide content to 5.9 mg/l. Cyanobacteria predominated in all biological zones of the microbial mat. The filamentous cyanobacteria of the genus Phormidium are the major mat-forming organisms, whereas unicellular cyanobacteria and the filamentous green bacterium Chloroflexus aurantiacus are minor components of the phototrophic communities. No cyanobacteria of the species Mastigocladus laminosus, typical of neutral and subacid springs, were identified. Seventeen species of both anoxygenic phototrophic bacteria and cyanobacteria were isolated from the microbial mats, most of which exhibited optimum growth at 20 to 45°C. The anoxygenic phototrophs were neutrophiles with pH optimum at about 7. The cyanobacteria were the most adapted to the alkaline conditions in the spring. Their optimum growth was observed at pH 8.5–9.0. As determined by the in situ radioisotope method, the optimal growth and decomposition rates were observed at 40–32°C, which is 10–15°C lower than the same parameter in the sulfide-deficient Octopus Spring (Yellowstone, United States). The maximum chlorophyll a concentration was 555 mg/m² at 40°C. The total rate of photosynthesis in the mats reached 1.3 g C/m² per day. The maximum rate of dark fixation of carbon dioxide in the microbial mats was 0.806 g C/m² per day. The maximum rate of sulfate reduction comprised 0.367 g S/m² per day at 40°C. The rate of methanogenesis did not exceed 1.188 g C/m² per day. The role of methanogenesis in the terminal decomposition of the organic matter was insignificant. Methane formation consumed 100 times less organic matter than sulfate reduction.     

Cedar Infestation Impacts Avian Communities along the Niobrara River Valley,Nebraska

Habitat modification has the potential to cause changes in structure and composition of bird communities. Our goal was to determine the response of Songbird community composition to eastern red cedar (Juniperus virginiana) removal in The Nature Conservancy's Niobrara Valley Preserve, Nebraska. We used point counts to survey birds in the riparian matrix of grassland and forest habitats. More than 60 species were recorded on surveys during 2004–2005. We also use the program PRESENCE to determine the response of five species to various habitat components, including cedar density: House Wren (Troglodytes aedon), Spotted Towhee (Pipilo maculates), Ovenbird (Seiurus aurocapillus), Red‐eyed Vireo (Vireo olivaceus), and Indigo Bunting (Passerina cyanea). Species richness estimates were highest in open and mixed habitat patches. Local populations of Ovenbirds and Red‐eyed Vireos responded positively to cedar density, whereas House Wren numbers declined as cedar density increased. Cedar abundance explained the most variation in bird community similarity between survey points; species richness increased as cedar density decreased. Habitat structure and composition drove variation in community composition and population abundance at fine, local scales within the Preserve. Fine‐scale management to remove cedar from local areas should increase diversity of avian species by maintaining a matrix of habitat types. Cedar removal at any scale will affect the composition of bird communities, and we encourage a structured approach to management decisions.     

Occurrence of enteroviruses in marine sediment along the coast of Barcelona, Spain

A survey of the occurrence of enteroviruses in marine sediment was undertaken in an area receiving polluted effluents. Enteroviruses were detected in 21 out of 38 samples (55%). Viruses were found as far as 5 km from the shoreline and at a depth of 82 m. Multiple correlations between enteroviruses and bacteria, detected in the same samples, were computed. No correlation could be demonstrated between virus numbers and any other parameter in sediment samples collected south of Barcelona. This lack of correlation is probably due to the different decay rates shown by bacteria and viruses. In contrast, the cases where pollution resulted from a more recent deposition, as in sediment samples collected north of Barcelona, enterovirus levels were correlated with fecal streptococci levels.     

6种交通重金属污染物在悬铃木叶、枝条组织中的分布研究

以南京市常见行道树二球悬铃木为试材,通过对交通繁忙区和相对清洁区道路两边悬铃木叶和一年生枝条中6种重金属元素在组织水平分布的研究,揭示其在悬铃木各组织中可能的分布机理,以及对重金属可能的抵御机制。结果表明,置于空气污染下悬铃木叶片与一年生枝条各组织具有累积重金属元素的能力,且污染区相对含量高于清洁区（除Ni外）;叶片各组织累积能力大小为下表皮＞上表皮、海绵组织＞栅栏组织。悬铃木一年生枝条表皮因具有皮孔、表皮毛和蜡质,故也有一定的重金属累积能力;悬铃木表皮系统是重要的重金属吸滞组织,且累积于表皮的重金属元素可通过表皮进入皮层和髓,这与一年生枝条内重金属元素的运输途径有关,具体运输机理有待于进一步探讨。根据悬铃木各组织重金属的分布,认为叶片和茎的表皮系统更能反映空气污染的真实情况,且这两种材料采集容易、破坏性小,建议在空气污染监测中大力采用。