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Casamayor E.O.,CSIC - Center for Advanced Studies of Blanes
Aquatic Microbial Ecology | Year: 2010

Vertical distributions of viable (most probable number, MPN) aerobic chemoautotrophic thiobacilli-like sulfur-oxidizing bacteria (ca. 70 samples in triplicate for MPN counts) and dark 14C-bicarbonate incorporation rates were analyzed in a series of sulfide-rich lakes. A special device for sampling sharply stratified populations on the scale of a few centimeters was used. Detailed analyses focused on the oxic-anoxic transition zone where aerobic sulfur-oxidizing bacteria should display positive chemotaxis, and in both fully oxic epilimnia and sulfide-rich anoxic hypolimnia. Kinetics of sulfide and thiosulfate potential oxidations in the presence of oxygen were followed in microcosm enrichments in one of the lakes. The highest MPN counts (>10 4 to 105 cells ml-1) were observed at the oxic-anoxic interfaces and in the depleted hypolimnia (1.3 μ 4.4 × 104 cells ml-1), whereas 1 order of magnitude lower concentrations were detected in the epilimnia (1.0 μ 2.3× 10 3 cells ml-1). Dark 14C-bicarbonate incorporation rates were higher at the oxic-anoxic interface (11.4 μ 9.5 μg C l-1 h-1) than in the hypolimnia (6.4 μ 5.9 μg C l-1 h-1) and epilimnia (1.0 μ 2.1 μg C l-1 h-1). A lack of correspondence between abundance of MPN thiobacilli, location at the sulfide interface, and dark carbon fixation rates was, however, consistently observed in a correlation analysis. Patterns of in situ potential aerobic thiosulfate oxidation did not match dark carbon fixation rates or MPN vertical distributions. The chemoautotrophic guild of these lakes emerged as a metabolically complex, taxonomically diverse group of aerobic, microaerophilic, and anaerobic microorganisms coexisting in the same lake. Thiobacilli may actively fix CO2 at certain depths but the question of which types of bacteria contribute most to dark CO2 fixation in the investigated lakes is still open, and the application of culture-independent molecular tools and single-cell analyses should be used to substantiate and further explore these findings. © Inter-Research 2010.

Barberan A.,CSIC - Center for Advanced Studies of Blanes | Casamayor E.O.,CSIC - Center for Advanced Studies of Blanes
Aquatic Microbial Ecology | Year: 2010

We aimed to identify phylogenetic community patterns in abundant planktonic bacteria (Alpha-, Beta-, and Gammaproteobacteria, Actinobacteria, Cyanobacteria, and Bacteroidetes) from a worldwide range of surface waters (lakes and seas-34 sites and ca. 4500 16S rRNA gene sequences). At each site we assessed the number of observed bacterial groups and the genetic relatedness of the most abundant groups through a community phylogenetic metaanalysis approach in order to (1) explore which potential ecological processes were consistent with the observed phylogenetic patterns in community assembly and (2) disentangle the effects of space and environment in β-diversity patterns for the different bacterial groups. Inland waters had significantly more bacterial groups and were more diverse than marine waters. Marine habitats showed a higher percentage of clustered sites than lakes, and bacterial communities were more closely related than expected by chance. Phylogenetic β-diversity analyses revealed different patterns to both salt composition (marine vs. inland salt lakes) and salt concentration for the dominant bacteria. We observed that while â-diversity patterns for Bacteroidetes were mostly shaped by salinity concentration, patterns in Alphaproteobacteria and Gammaproteobacteria were controlled by salt composition. Actinobacteria, Betaproteobacteria and Sphingobacteria were largely absent from marine habitats and from saline continental sites. In general and despite the lack of contextual metadata, environmental similarity was more relevant than spatial distribution for bacterial β-diversity patterns. However, we detected a geographic signal for some inland waters' groups (i.e. Actinobacteria, Beta-, and Gammaproteobacteria). Overall, the analyses indicated differences among phylogenetic groups and reflected patterns upon which further exploration of community assembly theory could be based. © Inter-Research 2010.

Barberan A.,University of Colorado at Boulder | Casamayor E.O.,CSIC - Center for Advanced Studies of Blanes | Fierer N.,University of Colorado at Boulder
Frontiers in Microbiology | Year: 2014

There has been a recent explosion of research within the field of microbial ecology that has been fueled, in part, by methodological improvements that make it feasible to characterize microbial communities to an extent that was inconceivable only a few years ago. Furthermore, there is increasing recognition within the field of ecology that microorganisms play a critical role in the health of organisms and ecosystems. Despite these developments, an important gap still persists between the theoretical framework of macroecology and microbial ecology. We highlight two idiosyncrasies of microorganisms that are fundamental to understanding macroecological patterns and their mechanistic drivers. First, high dispersal rates provide novel opportunities to test the relative importance of niche, stochastic, and historical processes in structuring biological communities. Second, high speciation rates potentially lead to the convergence of ecological and evolutionary time scales. After reviewing these unique aspects, we discuss strategies for improving the conceptual integration of microbes into macroecology. As examples, we discuss the use of phylogenetic ecology as an integrative approach to explore patterns across the tree of life. Then we demonstrate how two general theories of biodiversity (i.e., the recently developed theory of stochastic geometry and the neutral theory) can be adapted to microorganisms. We demonstrate how conceptual models that integrate evolutionary and ecological mechanisms can contribute to the unification of microbial ecology and macroecology. © 2014 Barberán, Casamayor and Fierer.

Auguet J.-C.,CSIC - Center for Advanced Studies of Blanes | Barberan A.,CSIC - Center for Advanced Studies of Blanes | Casamayor E.O.,CSIC - Center for Advanced Studies of Blanes
ISME Journal | Year: 2010

We have applied a global analytical approach to uncultured Archaea that for the first time reveals well-defined community patterns along broad environmental gradients and habitat types. Phylogenetic patterns and the environmental factors governing the creation and maintenance of these patterns were analyzed for c. 2000 archaeal 16S rRNA gene sequences from 67 globally distributed studies. The sequences were dereplicated at 97% identity, grouped into seven habitat types, and analyzed with both Unifrac (to explore shared phylogenetic history) and multivariate regression tree (that considers the relative abundance of the lineages or taxa) approaches. Both phylogenetic and taxon-based approaches showed salinity and not temperature as one of the principal driving forces at the global scale. Hydrothermal vents and planktonic freshwater habitats emerged as the largest reservoirs of archaeal diversity and consequently are promising environments for the discovery of new archaeal lineages. Conversely, soils were more phylogenetically clustered and archaeal diversity was the result of a high number of closely related phylotypes rather than different lineages. Applying the ecological concept of 'indicator species', we detected up to 13 indicator archaeal lineages for the seven habitats prospected. Some of these lineages (that is, hypersaline MSBL1, marine sediment FCG1 and freshwater plSA1), for which ecological importance has remained unseen to date, deserve further attention as they represent potential key archaeal groups in terms of distribution and ecological processes. Hydrothermal vents held the highest number of indicator lineages, suggesting it would be the earliest habitat colonized by Archaea. Overall, our approach provided ecological support for the often arbitrary nomenclature within uncultured Archaea, as well as phylogeographical clues on key ecological and evolutionary aspects of archaeal biology.

Macpherson E.,CSIC - Center for Advanced Studies of Blanes
Scientia Marina | Year: 2011

A new species of Munidopsis Whiteaves, 1874 is reported from the south of Crete, at 2046-2104 m, in the eastern Mediterranean Sea. The species (M. ariadne) is morphologically closely related to M. maunga Schnabel and Bruce, 2006, from New Zealand. The species is also close to M. polymorpha Koelbel, 1892, from Lanzarote, Canary Islands, and M. talismani A. Milne Edwards and Bouvier, 1894, from the NW Africa. The new species is described and illustrated and a diagnosis along with full illustration is provided for the latter 2 species.

Fernandez-Guerra A.,CSIC - Center for Advanced Studies of Blanes | Casamayor E.O.,CSIC - Center for Advanced Studies of Blanes
PLoS ONE | Year: 2012

Microorganisms mediating ammonia oxidation play a fundamental role in the connection between biological nitrogen fixation and anaerobic nitrogen losses. Bacteria and Archaea ammonia oxidizers (AOB and AOA, respectively) have colonized similar habitats worldwide. Ammonia oxidation is the rate-limiting step in nitrification, and the ammonia monooxygenase (Amo) is the key enzyme involved. The molecular ecology of this process has been extensively explored by surveying the gene of the subunit A of the Amo (amoA gene). In the present study, we explored the phylogenetic community ecology of AOB and AOA, analyzing 5776 amoA gene sequences from >300 isolation sources, and clustering habitats by environmental ontologies. As a whole, phylogenetic richness was larger in AOA than in AOB, and sediments contained the highest phylogenetic richness whereas marine plankton the lowest. We also observed that freshwater ammonia oxidizers were phylogenetically richer than their marine counterparts. AOA communities were more dissimilar to each other than those of AOB, and consistent monophyletic lineages were observed for sediments, soils, and marine plankton in AOA but not in AOB. The diversification patterns showed a more constant cladogenesis through time for AOB whereas AOA apparently experienced two fast diversification events separated by a long steady-state episode. The diversification rate (γ statistic) for most of the habitats indicated γAOA > γAOB. Soil and sediment experienced earlier bursts of diversification whereas habitats usually eutrophic and rich in ammonium such as wastewater and sludge showed accelerated diversification rates towards the present. Overall, this work shows for the first time a global picture of the phylogenetic community structure of both AOB and AOA assemblages following the strictest analytical standards, and provides an ecological view on the differential evolutionary paths experienced by widespread ammonia-oxidizing microorganisms. The emerged picture of AOB and AOA distribution in different habitats provides a new view to understand the ecophysiology of ammonia oxidizers on Earth. © 2012 Fernàndez-Guerra, Casamayor.

Bacardit M.,CSIC - Center for Advanced Studies of Blanes
Environmental science and pollution research international | Year: 2010

BACKGROUND, AIM, AND SCOPE: High mountain soils constitute a long-term cumulative record of atmospherically deposited trace elements from both natural and anthropogenic sources. The main aims of this study were to determine the level of major and trace metals (Al, Ti, Mn, Fe, and Zr) of lithologic origin and airborne contaminating trace elements (Ni, Cu, Zn, As, Cd, and Pb) in soils in the Central Pyrenees as an indication of background contamination over SW Europe, to establish whether there is a spatial pattern of accumulation of trace elements in soils as a function of altitude, and to examine whether altitude-related physicochemical properties of soils affect the accumulation of major metals and trace elements. METHODS: Major metals and trace elements were measured in "top" (i.e., first 10 cm) and "bottom" (i.e., below 10 cm) soil samples along an altitudinal transect (1,520-2,880 m a.s.l.) in the Central Pyrenees. Total concentrations were determined by X-ray fluorescense spectrometry. Total major metal concentrations were analysed by conventional X-ray fluorescence spectrometry (XRF) with a Siemens SRS 303 instrument. Total trace element concentrations were determined with an energy-dispersive multielement miniprobe XRF analyser. Acid-extractable concentrations were measured by inductively coupled plasma after previous extraction with nitric acid and hydrogen peroxide in closed beakers. Acid-extractable major metal concentrations were measured by inductively coupled plasma (ICP)-Optic Emission Spectrometry with a Perkin Elmer 3200 RL Instrument. Acid-extractable trace element concentrations were determined by ICP-Mass Spectrometry with a Perkin Elmer ELAN 6000. RESULTS: Trace element concentration ranges were (in mg kg(-1), inventories in g m(-2) between parenthesis) <2-58 (0.5-6.6) for Ni, 6-30 (0.2-3.4) for Cu, 38-236 (1.6-32.4) for Zn, 6-209 (0.2-12.8) for As, 0.02-0.64 (<0.04) for Cd, and 28-94 (0.6-13.0) for Pb. These concentrations were, in general, comparable to those recorded in soils from other European mountainous areas and were in many cases above the threshold recommended for ecosystem protection by regional and European environmental authorities. The highest concentrations were found at lower altitudes, indicating an effect of local contamination up to ∼2,300 m a.s.l. Only above this altitude can trace elements in soils be considered representative of a background, long-range atmospheric contamination. CONCLUSIONS: None of the storage capacity properties of soils examined were determinant of the differences in elemental concentrations along the altitudinal transect. At the upper altitude range, Ni, Cu, and Pb showed a approximately two- to fivefold increase over the average concentration of the local dominant lithology, reflecting the regional and global background of atmospheric contamination in the area.

Camarero L.,CSIC - Center for Advanced Studies of Blanes | Catalan J.,CSIC - Center for Advanced Studies of Blanes
Nature Communications | Year: 2012

Recent findings indicate that increased atmospheric deposition of nitrogen of human origin has caused changes in the pattern of ecological nutrient limitation in lakes in the northern hemisphere. An increase in the nitrogen to phosphorus ratio, and hence a shift from pristine nitrogen limitation to human-induced phosphorus limitation of phytoplankton growth, seems to have been driven by deposition of atmospheric nitrogen. These findings challenge the classical paradigm of lake phytoplankton productivity being naturally limited by phosphorus availability. However, atmospheric phosphorus deposition may also be highly relevant. Here we show how dissolved inorganic nitrogen concentration has decreased in the Pyrenean lake district over recent decades, despite there being an increase in deposition of atmospheric nitrogen. This is related to an increased atmospheric phosphorus load in the lake water, as a result of higher atmospheric inputs. These changes are causing phytoplankton to revert from being phosphorus-limited to being nitrogen-limited. © 2012 Macmillan Publishers Limited. All rights reserved.

Barberan A.,CSIC - Center for Advanced Studies of Blanes | Bates S.T.,University of Colorado at Boulder | Casamayor E.O.,CSIC - Center for Advanced Studies of Blanes | Fierer N.,University of Colorado at Boulder
ISME Journal | Year: 2012

Exploring large environmental datasets generated by high-throughput DNA sequencing technologies requires new analytical approaches to move beyond the basic inventory descriptions of the composition and diversity of natural microbial communities. In order to investigate potential interactions between microbial taxa, network analysis of significant taxon co-occurrence patterns may help to decipher the structure of complex microbial communities across spatial or temporal gradients. Here, we calculated associations between microbial taxa and applied network analysis approaches to a 16S rRNA gene barcoded pyrosequencing dataset containing >160 000 bacterial and archaeal sequences from 151 soil samples from a broad range of ecosystem types. We described the topology of the resulting network and defined operational taxonomic unit categories based on abundance and occupancy (that is, habitat generalists and habitat specialists). Co-occurrence patterns were readily revealed, including general non-random association, common life history strategies at broad taxonomic levels and unexpected relationships between community members. Overall, we demonstrated the potential of exploring inter-taxa correlations to gain a more integrated understanding of microbial community structure and the ecological rules guiding community assembly. © 2012 International Society for Microbial Ecology All rights reserved.

Blanquer A.,CSIC - Center for Advanced Studies of Blanes | Uriz M.J.,CSIC - Center for Advanced Studies of Blanes
BMC Evolutionary Biology | Year: 2010

Background. Rare species have seldom been studied in marine habitats, mainly because it is difficult to formally assess the status of rare species, especially in patchy benthic organisms, for which samplings are often assumed to be incomplete and, thus, inappropriate for establishing the real abundance of the species. However, many marine benthic invertebrates can be considered rare, due to the fragmentation and rarity of suitable habitats. Consequently, studies on the genetic connectivity of rare species in fragmented habitats are basic for assessing their risk of extinction, especially in the context of increased habitat fragmentation by human activities. Sponges are suitable models for studying the intra- and inter-population genetic variation of rare invertebrates, as they produce lecitotrophic larvae and are often found in fragmented habitats. Results. We investigated the genetic structure of a Mediterranean sponge, Scopalina lophyropoda (Schmidt), using the allelic size variation of seven specific microsatellite loci. The species can be classified as "rare" because of its strict habitat requirements, the low number of individuals per population, and the relatively small size of its distribution range. It also presents a strong patchy distribution, philopatric larval dispersal, and both sexual and asexual reproduction. Classical genetic-variance-based methods (AMOVA) and differentiation statistics revealed that the genetic diversity of S. lophyropoda was structured at the three spatial scales studied: within populations, between populations of a geographic region, and between isolated geographic regions, although some stochastic gene flow might occur among populations within a region. The genetic structure followed an isolation-by-distance pattern according to the Mantel test. However, despite philopatric larval dispersal and fission events in the species, no single population showed inbreeding, and the contribution of clonality to the population makeup was minor (only ca. 4%). Conclusions. The structure of the S. lophyropoda populations at all spatial scales examined confirms the philopatric larval dispersal that has been reported. Asexual reproduction does not seem to play a relevant role in the populations. The heterozygote excess and the lack of inbreeding could be interpreted as a hitherto unknown outcrossing strategy of the species. The envisaged causes for this strategy are sperm dispersal, a strong selection against the mating of genetically related individuals to avoid inbreeding depression or high longevity of genets combined with stochastic recruitment events by larvae from other populations. It should be investigated whether this strategy could also explain the genetic diversity of many other patchy marine invertebrates whose populations remain healthy over time, despite their apparent rarity. © 2010 Blanquer and Uriz; licensee BioMed Central Ltd.

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