Prokaryotic community composition and ecology of floating macroscopic filaments from an extreme acidic environment, Río Tinto (SW, Spain)

The prokaryotic diversity of macroscopic filaments located at the water surface in an extreme acidic environment, Río Tinto (SW, Spain), has been analysed through denaturing gradient gel electrophoresis (DGGE), cloning of 16S rRNA genes and fluorescence in situ hybridization (FISH). The dominant species present in the macrofilaments were Acidithiobacillus ferrooxidans, Leptospirillum ferrooxidans and Acidiphilium spp., which represented the three main bacterial genera found in the water column of the river. However, our results also showed the presence of other microorganisms not previously detected in the Río Tinto. Within the Gammaproteobacteria class, sequences closely related to the iron-oxidizing bacteria WJ2 and DSM 2392 were found, as well as sequences related to the non-acidophilic genera Aeromonas and Acinetobacter. In addition, two other new phylotypes related to Gram-positive species from the genera Desulfosporosinus, Clostridium and Mycobacterium were identified. The presence of these anaerobic microorganisms strongly suggests that the filaments could originate in the deeper parts of the river as a typical acid streamer attached to the rocks or the sediments and be pulled up towards the surface when they reach certain buoyancy.     

Distribution and seasonal variability in the benthic eukaryotic community of Río Tinto (SW, Spain), an acidic, high metal extreme environment

The eukaryotic community of the Río Tinto (SW, Spain) was surveyed in fall, winter and spring through the combined use of traditional microscopy and molecular approaches, including Denaturing Gradient Gel Electrophoresis (DGGE) and sequence analysis of 18S rRNA gene fragments. Eukaryotic assemblages of surface sediment biofilms collected in January, May and September 2002 were compared from 13 sampling stations along the river. Physicochemical data revealed extremely acidic conditions (the pH ranged from 0.9 to 2.5) with high concentrations of heavy metals, including up to 20 mg l(-1) Fe, 317 mg l(-1) Zn, 47 mg l(-1) As, 42 mg l(-1) Cd and 4 mg l(-1) Ni. In total, 20 taxa were identified, including members of the Bacillariophyta, Chlorophyta and Euglenophyta phyla as well as ciliates, cercomonads, amoebae, stramenopiles, fungi, heliozoans and rotifers. In general, total cell abundances were highest in fall and spring but decreased drastically in winter, and the sampling stations with the most extreme conditions showed the lowest number of cells, as well as the lowest diversity. Species diversity did not vary much during the year. Only the filamentous algae showed a dramatic seasonal change, since they almost disappeared in winter and reached the highest biomass during the summer. Principal Components Analysis (PCA) showed a high inverse correlation between pH and most of the heavy metals analyzed, as well as Dunaliella sp., while Chlamydomonas sp. was directly related to pH during May and September. Three heavy metals (Zn, Cu and Ni) remained separate from the rest and showed an inverse correlation with most of the species analyzed, except for Dunaliella sp.     

Microbial community structure across the tree of life in the extreme Río Tinto

Understanding biotic versus abiotic forces that shape community structure is a fundamental aim of microbial ecology. The acidic and heavy metal extreme Río Tinto (RT) in southwestern Spain provides a rare opportunity to conduct an ecosystem-wide biodiversity inventory at the level of all three domains of life, because diversity there is low and almost exclusively microbial. Despite improvements in high-throughput DNA sequencing, environmental biodiversity studies that use molecular metrics and consider entire ecosystems are rare. These studies can be prohibitively expensive if domains are considered separately, and differences in copy number of eukaryotic ribosomal RNA genes can bias estimates of relative abundances of phylotypes recovered. In this study we have overcome these barriers (1) by targeting all three domains in a single polymerase chain reaction amplification and (2) by using a replicated sampling design that allows for incidence-based methods to extract measures of richness and carry out downstream analyses that address community structuring effects. Our work showed that combined bacterial and archaeal richness is an order of magnitude higher than eukaryotic richness. We also found that eukaryotic richness was highest at the most extreme sites, whereas combined bacterial and archaeal richness was highest at less extreme sites. Quantitative community phylogenetics showed abiotic forces to be primarily responsible for shaping the RT community structure. Canonical correspondence analysis revealed co-occurrence of obligate symbionts and their putative hosts that may contribute to biotic forces shaping community structure and may further provide a possible mechanism for persistence of certain low-abundance bacteria encountered in the RT.     

Refuge from predation, the benefit of living in an extreme acidic environment?

Organisms living in extreme habitats require costly adaptations to cope with these conditions. Among the suggested potential benefits that trade off these costs is refuge from predation. To study these interactions in extreme environments, samples were taken in the cave Cueva de Villa Luz, Tabasco, Mexico, where more than 32 subterranean springs, some H(2)S rich, rise from the floor. Hydrogen sulfide gas plus oxygen is absorbed by freshwater, and oxidation forms concentrated sulfuric acid. Snottites, whitish hollow mucous tubes, hang from the ceiling of the cave. Fluid drops from these snottites were recorded as having pH values of 0-3. We report the discovery of a new species of nematode that thrives in the highly acidic environment of the snottite. Micro CT scan of snottites reveals a complex interaction between the acidic snottite, nematodes, and abundant nematode-eating mites. The nematode adaptation to low pH probably protects them against mite predation, for which nematodes are most likely the most important source of carbon in this sulfur-driven ecosystem.     

Metal Accumulation Screening of the Río Tinto Flora (Huelva,Spain)

Río Tinto (Huelva, Spain) is located in one of the most important mining regions in the world. Its soils are characterized by their extreme acidity and elevated concentrations of heavy metals. Due to these characteristics, the Tinto ecosystem is considered unique and an ideal location to study biological adaptations to this type of habitat. Plant species that present these adaptations might be useful to mining and other metal pollution restoration programs. This study reports the results for the screening of Ca, Mg, Na, Mn, Fe, Ni, Cu, Zn, As, and Pb in aerial tissues of 97 plant species from the Tinto basin flora. In addition, plant–soil relationships were analyzed using the biological absorption coefficient (BAC) to detect the main plant adaptations in the Tinto flora. The species selected are representative of the biomass of the main dominant edaphophile and climatophile vegetation communities of the three river sections, forest, and subseral stages. Plant and soil elemental analyses were performed using inductively coupled plasma–mass spectrometry technique (ICP-MS). The results indicate that in general, Tinto flora shows a pattern of accumulation of the analyzed elements in aerial tissues which agrees with the nutritional requirements of vascular plants (macronutrients > micronutrients > indifferent or toxic elements). Among macronutrients, Ca seems to be an essential element in this habitat. This element accumulates in the aerial plant tissues. Basically, the Río Tinto flora is made of Fe, Cu, Zn, Ni, As, and Pb excluders, although some analyzed species of Erica, Quercus, Lavandula, Cistus, Genista, and Cytisus genera can be considered Mn accumulators. The results of this study make up a body of fundamental knowledge of the strategies used by plants to thrive in habitats with high concentrations of toxic heavy metals. This information is vital when it comes to planning a restoration program. Plants must be selected and used according to the requirements, always respecting the characteristics of the territory and facilitating the development of suitable vegetation.     

Detection of Peptidic Sequences in the Ancient Acidic Sediments of Río Tinto,Spain

Biomarkers are molecules that are produced by or can be associated with biological activities. They can be used as tracers that give us an idea of the ancient biological communities that produced them, the paleoenvironmental conditions where they lived, or the mechanism involved in their transformation and preservation. As a consequence, the preservation potential of molecules over time depends largely on their nature, but also on the conditions of the environment, which controls the decomposition kinetics. In this context, proteins and nucleic acids, which are biomolecules bearing biological information, are among the most labile molecules. In this research, we report the presence of short-chained peptides obtained from extracts of ferruginous sedimentary deposits that have been produced under the acidic and oxidizing solutions of Río Tinto, Spain. These preliminary results go against the paradigmatic idea that considers the acidic and oxidizing environments inappropriate for the preservation of molecular information.     

Development and Structure of Eukaryotic Biofilms in an Extreme Acidic Environment,Río Tinto (SW,Spain)

An in situ colonization assay was performed to study the early stages of biofilm formation in Río Tinto (SW, Spain), an extremely acidic environment (pH ca. 2). Eukaryotic assemblages were monitored at monthly intervals for 1 year. Diversity, colonization rates, and seasonal variations were analyzed. Structural features of naturally grown biofilms were explored by light and scanning electron microscopy in backscattered electron mode. A total of 14 taxa were recognized as constituents of the eukaryotic assemblages. The eukaryotic communities were dissimilar at the different sampling sites. The lowest diversity was found at the most extreme locations, in terms of pH and heavy metal concentrations. The biofilms were mainly formed by species from the genera Dunaliella and Cyanidium. Two genera of filamentous algae, Zygnemopsis and Klebsormidium, were principally responsible for the variability in the cell number throughout the year. These species appear in June to decrease almost completely between October and November. In contrast, the number of heterotrophic flagellates and ciliates remained constant throughout the year. The microcolonization sequence showed an initial accumulation of amorphous particles composed of bacteria and inorganic grains of minerals. By the end of the second month, the organic matrix was also populated by fungi, bacteria, and a few eukaryotic heterotrophs such as amoebae and small flagellates. Diatoms only showed significant colonization in regions where mycelial matrices were first established. Flagellated green algae such as Dunaliella or Chlamydomonas as well as Euglena were also present at the very beginning of the biofilm development, although in low numbers (<100 cells cm^–2). After the flagellated cells, sessile species of algae such Chlorella or Cyanidium appeared. Filamentous algae were the last species to colonize the biofilms. Most of the naturally grown biofilms were found to be structures composed of different species organized in different layers separated, probably by extracellular polymeric substances, although more analysis should be done in this regard. The possible implications of the biofilm structure in the adaptation to this extreme habitat are discussed.     

The distribution and ecology of littoral Oligochaeta and Aphanoneura (Annelida) of the Natural and Historical Reserve of Isla Martín García,Río de la Plata River,Argentina

The objective of this paper is to provide data on the distribution and ecology of oligochaetes and aphanoneurans occurring in the Río de la Plata, Argentina, including details regarding, their densities, faunal characteristics, species richness, diversity and equitability. Between 1995 and 1997, a total of five stations on the Río de la Plata were sampled on eight different occasions. The taxocenosis of Oligochaeta and Aphanoneura included 30 species belonging in six families: Naididae, Tubificidae, Narapidae, Enchytraeidae, Lumbricidae and Aeolosomatidae. The density varied between 44495 ind m^–2 and 57 ind m^–2. Species richness varied between 1 and 17, the diversity ranged from 0.07 to 2.55, and equitability varied between 0.08 and 0.64. According to dominance and frequency, the dominant, constant and widely distributed species were: Nais variabilis, Stephensoniana trivandrana, Amphichaeta leydigi, Chaetogaster diastrophus, Limnodrilus hoffmeisteri, Aulodrilus pigueti, Narapa bonettoi and the species of Enchytraeidae and Aeolosomatidae.     

Farming,fishing, and fire in the history of the upper Río Negro region of Venezuela

Studies of Río Negro subsistence farming and fishing activities are used to estimate the human carrying capacity for the region and the likely pattern of human land-use during prehistory. Ceramic evidence suggests human presence in the region more than 3000 years ago. Traditional farming is labor intensive and relatively unproductive. Nevertheless, farmers achieve an energy return of 15.21, and produce 2600 kcal per work hour. Fish are the major protein source, but fish catch per unit of effort and fish yield per hectare of floodplain are very low; fishermen are probably exploiting local fish resources very close to their limit. The low human population density would suggest that the Río Negro forest has been relatively undisturbed. Nevertheless, charcoal is widespread and abundant in forest soils. This charcoal is probably from anthropogenic or natural wildfires. These results suggest a much more complex history for Amazonia than previously thought.K. Clark is a free-lance biologist residing in Lima, Peru     

Contrasting Microbial Community Assembly Hypotheses: A Reconciling Tale from the Río Tinto

Background

The Río Tinto (RT) is distinguished from other acid mine drainage systems by its natural and ancient origins. Microbial life from all three domains flourishes in this ecosystem, but bacteria dominate metabolic processes that perpetuate environmental extremes. While the patchy geochemistry of the RT likely influences the dynamics of bacterial populations, demonstrating which environmental variables shape microbial diversity and unveiling the mechanisms underlying observed patterns, remain major challenges in microbial ecology whose answers rely upon detailed assessments of community structures coupled with fine-scale measurements of physico-chemical parameters.

Methodology/Principal Findings

By using high-throughput environmental tag sequencing we achieved saturation of richness estimators for the first time in the RT. We found that environmental factors dictate the distribution of the most abundant taxa in this system, but stochastic niche differentiation processes, such as mutation and dispersal, also contribute to observed diversity patterns.

Conclusions/Significance

We predict that studies providing clues to the evolutionary and ecological processes underlying microbial distributions will reconcile the ongoing debate between the Baas Becking vs. Hubbell community assembly hypotheses.     

Metal Uptake and Distribution in Cultured Seedlings of Nerium oleander L. (Apocynaceae) from the Río Tinto (Huelva, Spain)

Nerium oleander L. (Apocynaceae) is a micro-nano phanerophyte that grows in the riverbanks of the Río Tinto basin (Southwest Iberian Peninsula). The waters and soils of the Río Tinto area are highly acidic and have high concentrations of heavy metals. In this environment, N. oleander naturally grows in both extreme acidic (EA) and less extreme acidic (LEA) water courses, excluding, and bioindicating certain metals. In this work, we compared and evaluated the accumulation preferences and capacities, the distribution and processes of biomineralization of metals (Fe, Cu, Zn, Mn, Mg, Ca) in the first stages of growth of EA and LEA oleanders by means of inductively coupled plasma–mass spectrometry, scanning electron microscopy, and energy dispersive X-ray analyzer analysis. Seeds from both environments were grown and treated with a self-made solution simulating the most extreme red waters from the Río Tinto. LEA plants drastically reduces the metal uptake at the beginning, but later reactivates the uptake reaching concentration values in the same range as the EA plants. The results showed high Mn, Zn and Mg concentrations, accumulation of Fe and Cu in plants from both environments, differing from the metal concentrations of field-grown oleanders. Iron bioformations with traces of other metals were present inside and over epidermal cells and inside vascular cells of stems and roots. They were absent of leaves. The accumulation properties of N. oleander in its early stages of development make it a species to take in consideration in phytoremediation processes but optimized conditions are needed to ensure enough biomass production.     

Land use effects on erosion and carbon storage of the Río Chimbo watershed, Ecuador

Background and aims

Soil carbon storage is an important component of global carbon cycling. Andean Andisols have high carbon content and are vulnerable to erosion because of agricultural intensification and deforestation. This study examines the effects of land use on erosion and soil carbon storage in the Río Chimbo watershed of Ecuador.

Methods

Soil carbon content, age, and erosion estimated from ¹³⁷Cs inventories was measured along an elevational transect under annual cropping, natural forest, páramo, pasture, and tree plantations.

Results

Land use, particularly annual cropping, affected ¹³⁷Cs levels in the upper soil layers, but did not have an impact on total carbon storage to a depth of 1 m. Relative erosion rates estimated from ¹³⁷Cs inventories at sites under annual cropping averaged 27 t ha^?1?y^?1 over the erosion rate of non-cultivated sites. A linear relationship was observed between soil carbon age (determined by ¹⁴C levels) and ¹³⁷Cs levels, where pasture sites had lower ¹³⁷Cs and older carbon compared to natural forest sites.

Conclusions

The effects of land use on soil loss in the Río Chimbo watershed suggest a loss and/or removal of soil carbon, particularly under annual cropping.     

Distribution,status and biology of the tortoise,Geochelone chilensis,in Río Negro Province,Argentina

Morphometric and meristic data from 32 specimens from Río Negro Province do not allow differentiation between G. donosobarrosi and G. chilensis. The significance of morphological and genetic differentiation among Argentinian tortoises is yet to be determined; southern Chaco tortoises undergo ontogenetic and sexual dichromatism. Geochelone chilensis has an extensive latitudinal range (Map 1). Field investigations indicate that Chaco tortoises occupy, and apparently excavate, burrows in the southern portion of the range, prior reports of the species’ southern limit are evaluated and the link between tortoise distribution and “monte”; vegetation is discussed. The season of reproduction and clutch size are noted. Extensive internal pet traffic has markedly affected tortoise populations in some areas; near the southern limit of the range, however, there is little commercial collecting.     

Mechanical aquatic weed management in the lower valley of the Río Negro, Argentina

A major irrigation system in the Lower Valley of the Rió Negro, Argentina, has been invaded by aquatic plants, with Potamogeton illinoensis Morong dominant in irrigation channels and Potamogeton pectinatus L. dominant in drainage channels. Although several other macrophytes are present, problems are largely caused by the dominant species. Results are presented for plant biomass response to weed control treatments using a chain-cutting method in the principal irrigation channel of the system. Peak above-ground biomass of Potamogeton illinoensis was reduced by about 38% by this physical control regime. The treated populations regrew rapidly after spring clearance, but did not regrow after subsequent mid- and late-season clearance operations, even though untreated population biomass remained high during this period. The highest density of Potamogeton illinoensis ramets was found in treated areas. Chain- cutting produced no discernible effect on dissolved oxygen, water temperature, water conductivity, pH or light extinction coefficient compared with untreated check sectors of the channel.     

Distribution of fishes in the Río Guayalejo-Río Tamesí system and relationships with environmental factors in northeastern Mexico

A priority issue in ecology and biogeography is understanding the patterns in species diversity and the causal factors of their distribution, which allows the generation of information for conservation strategies. The longitudinal distribution of fishes and their relationships with environmental variables were studied in the Guayalejo-Río Tamesí system (northeastern Mexico) from February 2000 to July 2001. A total of 5918 fish were caught in 27 collections along an altitudinal gradient in the main river course, from high mountain (1500 masl) to coastal plain near Tampico. Forty-three native and five exotic species, belonging to 35 genera in 23 families, were identified. Cluster analyses identified four major fish habitats in the river system. A distinctive euryhaline marine fish habitat (1) occurs near the mouth with native and two exotic species. Two other habitats consist essentially of freshwater fish species that are distributed along the longitudinal gradient. One of these habitats (habitat 4) shows greater diversity, as per the Shannon index value, and also includes amphidromous fish, in addition to two exotic freshwater fish; the other (habitat 2) includes freshwater, euryhaline and three exotic species. The changes in the frequency of occurrence and the abundance of Gambusia vittata, Astyanax mexicanus, and Xiphophorus variatus contribute to explaining differences between these habitats. Another habitat (3) is represented by two sampling sites located near the mouth and consist of freshwater and euryhaline fish and three exotic cyprinids with broad salinity tolerance. The low abundance and richness of exotic species suggest little impact on native fish fauna in this river. The fish assemblage of the Guayalejo-Tamesí river system species changes along a longitudinal gradient with the addition, replacement and presence of indicator species. Upstream fish fauna is mostly composed of freshwater species, some of them generalists that inhabit the entire longitudinal gradient, others that are restricted to certain sites, and the remainder of species is an assemblage composed of a mixture of euryhaline freshwater and marine species near the mouth.     

Field observations of the golden-mantled tamarin, Saguinus tripartitus, on the Río Curaray, Peruvian Amazonia

During a primatological survey on the Río Curaray in north-eastern Peruvian Amazonia, observations on the ecology and behaviour of the golden-mantled tamarin, Saguinus tripartitus, were made. Two groups consisting of 6 and 9 individuals were observed. The diet of one group that was observed in some detail consisted of fruit, insects (tettigoniid orthopterans) and gums. Patterns of height use were very similar to those observed in saddle-back tamarins, Saguinus fuscicollis. This similarity and the lack of evidence for sympatry with either S. fuscicollis or S. nigricollis lead to the suggestion that S. tripartitus should be reconsidered as a subspecies of S. fuscicollis rather than a species on its own; alternatively, other subspecies of S. fuscicollis should be raised in taxonomic rank.     

Ecology,morphology and physiology of Chroothece richteriana (Rhodophyta,Stylonematophyceae) in the highly calcareous Río Chícamo,south-east Spain

The ecology of Chroothece was studied in the highly calcareous Río Chícamo, south-east Spain, in order to explain its success there, but rarity elsewhere. The river, which originates mainly from an underground aquifer, has water with high conductivity, sulphate and nitrate but low phosphate concentrations, the latter mainly organic. Chroothece occurs in mats and in lobed colonies reaching 4 cm in the broadest dimension. The colony surface consists of one layer of cells, each of which is attached to a stalk, which dichotomizes when the cell divides; stalks often extend to the colony base. The central region of many mat cells and almost all colony cells has a yellow to orange-brown colour, associated with the numerous lipid droplets densely covering the surface of the pyrenoid and arms of the star-shaped chloroplast. Field material and laboratory isolates indicate that stalk formation occurs under moderate P limitation and both stalks and cell sheath show high phosphatase activities. This also occurred in a culture collection strain maintained for 30 years in a very P-rich medium, but then transferred to a moderately P-limiting medium (c. 0.9 mg l^?1). We suggest that colony formation is initiated by aggregation of motile cells following P pulses in the water. Comparisons are made with Rivularia, a competitor in this nitrate-rich river, in spite of being a N₂-fixer. One difference is that Chroothece cells lie at the periphery of the colonies and are therefore exposed to maximum sunlight, whereas Rivularia trichomes grow inside colonies with photoprotection by scytonemin. However, the ability to withstand heavy grazing pressure may be an especially important factor favouring Rivularia here.     

Spatial and seasonal distribution patterns of fish assemblages in the Río Champotón, southeastern Mexico

Río Champotón in the Yucatán Peninsula is within the Usumacinta Province, the most diverse in fish fauna in Mexico, and is part of the Mesoamerican hotspot, with high endemism and exceptional habitat loss. The spatial and seasonal variability of its fish fauna and their relation to physical habitat characteristics were studied, finding 53 taxa. Canonical correspondence analysis shows salinity, distance from the river mouth, and substratum type differentiate an estuarine and a freshwater region. Fish fauna replacement was observed, with taxa exclusive to each region: 26 estuarine and 27 freshwater species. Six freshwater species enter the estuarine region when the high river flow depletes salinity. Estuary showed greater seasonal differences in specific richness than the freshwater region, which have sites with higher local specific richness. Despite its small drainage, Río Champotón has a highly diverse fish fauna and some areas are affected by human activity and the hurricane season. Its conservation is of critical importance.     

Comparative molecular biological analysis of the microbial community of the Holocene and Pleistocene deposits of Posol’skaya Shoal,Lake Baikal

The bacterial diversity was studied in sediment layers of Posol’skaya Shoal station (Southern Baikal) belonging to different periods. A set of primers specific to individual bacterial groups was used to analyze the 16S rRNA gene fragments. The bacterial diversity in the Holocene deposits was found to be higher than in the Pleistocene ones. In the upper sediments, a positive PCR reaction with bacterial primers and with specific cyanobacterial and archaebacterial primers was detected. The following phylogenetic groups were revealed in the microbial community of the surface horizon: green nonsulfur bacteria, δ-proteobacteria, β-proteobacteria (Nitrospirae), α-proteobacteria, acidobacteria, crenarchaeota, euryarchaeota, and groups of uncultured bacteria. From the DNA of the Pleistocene deposits, the PCR product was obtained only with bacterial primers. The representatives of the genus Pseudomonas were most closely related to the sequences obtained (95–97% homology).