Biogeochemistry of a deep-sea whale fall: sulfate reduction, sulfide efflux and methanogenesis

Deep-sea whale falls create sulfidic habits Supporting chemoautotrophic communities, but microbial processes underlying the formation Of Such habitats remain poorly evaluated. Microbial degradation processes (sulfate reduction, methanogenesis) and biogeochemical gradients were studied in a whale-fall habitat created by a 30 t whale carcass deployed at 1675 m depth for 6 to 7 yr on the California margin. A variety of measurements were conducted including photomosaicking, microsensor measurements, radio-tracer incubations and geochemical analyses. Sediments were Studied at different distances (0 to 9 in) from the whale fall. Highest microbial activities and steepest vertical geochemical gradients were found within 0.5 m of the whale fall, revealing ex situ sulfate reduction and in vitro methanogenesis rates of up to 717 and 99 mmol m(-2) d(-1), respectively. In sediments containing whale biomass, methanogenesis was equivalent to 20 to 30%, of sulfate reduction. During in vitro sediment studies, sulfide and methane were produced within days to weeks after addition of whale biomass, indicating that chemosynthesis is promoted at early stages of the whale fall. Total sulfide production from sediments within 0.5 m of the whale fall was 2.1 +/- 3 and 1.5 +/- 2.1 mol d(-1) in Years 6 and 7, respectively, of which similar to 200 mmol d(-1) were available as free sulfide. Sulfate reduction in bones was much lower, accounting for a total availability of similar to 10 mmol sulfide d(-1). Over periods of at least 7 yr, whale falls can create sulfidic conditions similar to other chemosynthetic habitats Such as cold seeps and hydrothermal vents.

Biogeochemistry of an Amazonian podzol-ferralsol soil system with white kaolin

The podzol-ferralsol soil systems, which cover great areas of Amazonia and other equatorial regions, are frequently associated with kaolin deposits and store and export large amounts of carbon. Although natural organic matter (NOM) plays a key role in their dynamics, little is known about their biogeochemistry. In order to assess the specific role of dissolved organic matter (DOM) on NOM storage in deep horizons and to determine possible relationships between kaolin formation and DOM properties, we studied the groundwater composition of a typical podzol-ferralsol soil catena from the Alto Rio Negro region, Brazil. Groundwater was sampled using tension-free lysimeters placed according to soil morphology. DOC, E-H, p(H), and dissolved Si, Al3+, Fe2+, and Fe3+ were analyzed for all samples and values are given in a database. Quantification of other dissolved ions, small carboxylic acids and SUVA(254) index and acid-base microtitration was achieved on selected samples. Part of the DOM produced by the hydromorphic podzols is directly exported to the blackwater streams; another part percolates at greater depth, and more than 90% of it adsorbs in the Bh-Bhs horizons, allowing carbon storage at depth. Humic substances are preferentially adsorbed with regard to small carboxylic compounds. With regard to kaolin genesis, kaolinite precipitation is favored by Al release from NOM mineralization within the Bh-Bhs and kaolin bleaching is ensured by iron reduction due to acidity and relatively low E-H. Fe2+ mobility can be related to small E-H variations and enhanced by the significant concentration of small carboxylic acids. The long-term result of these processes is the thickening of the kaolin, and it can be inferred that kaolin is likely to occur where active, giant podzols are close to a slope gradient sufficient enough to lower the deep water table.

Accumulation of six metals in the mangrove crab Ucides cordatus (Crustacea: Ucididae) and its food source, the red mangrove Rhizophora mangle (Angiosperma: Rhizophoraceae)

The crab Ucides cordatus and the red mangrove Rhizophora mangle are endemic mangrove species and potential bio-accumulators of metals. This study quantified the accumulation of six metals (Cd, Cr, Cu, Hg, Mn and Pb) in different organs (claw muscle, hepatopancreas and gills) of U. cordatus, as well as in different maturation stages of the leaves (buds, green mature, and pre-abscission senescent) of R. mangle. Samples were collected from mangrove areas in Cubatao, state of Sao Paulo, a heavily polluted region in Brazil. Data for metal contents in leaves were evaluated by one-way ANOVA; while for crabs a factorial ANOVA was used to investigate the effect of different tissues, animal size and the interactions between them. Means were compared by Tukey test at five percent, and the association between the metal concentrations in each crab organ, depending on the size, was evaluated by Pearson's linear correlation coefficient (r). Concentrations of Pb and Hg were undetectable for the different leaf stages and crab tissues, while Cd concentrations were undetectable in the leaf stages. In general, the highest accumulation of metals in R. mangle leaves occurred in pre-abscission senescent and green mature leaves, except for Cu, which was found in the highest concentrations in buds and green mature leaves. For the crab, Cd, Cu, Cr and Mn were present in concentrations above the detection limit, with the highest accumulation in the hepatopancreas, followed by the gills. Cu was accumulated mostly in the gills. Patterns of bioaccumulation between the crab and the mangrove tree differed for each metal, probably due to the specific requirements of each organism for essential metals. However, there was a close and direct relationship between metal accumulation in the mangrove trees and in the crabs feeding on them. Tissues of R. mangle leaves and U. cordatus proved effective for monitoring metals, acting as important bioindicators of mangrove areas contaminated by various metals. (C) 2012 Elsevier Inc. All rights reserved.

Genetic transformation of Diaporthe phaseolorum, an endophytic fungus found in mangrove forests, mediated by Agrobacterium tumefaciens

We describe the genetic transformation of the mycelial tissue of Diaporthe phaseolorum, an endophytic fungus isolated from the mangrove species Laguncularia racemosa, using Agrobacterium tumefaciens-mediated transformation (ATMT). ATMT uses both the hygromycin B resistant (hph) gene and green fluorescent protein as the selection agents. The T-DNA integration into the fungal genome was assessed by both PCR and Southern blotting. All transformants examined were mitotically stable. An analysis of the T-DNA flanking sequences by thermal asymmetric interlaced PCR (TAIL-PCR) demonstrated that the disrupted genes in the transformants had similarities with conserved domains in proteins involved in antibiotic biosynthesis pathways. A library of 520 transformants was generated, and 31 of these transformants had no antibiotic activity against Staphylococcus aureus, an important human pathogen. The protocol described here, using ATMT in D. phaseolorum, will be useful for the identification and analysis of fungal genes controlling pathogenicity and antibiotic pathways. Moreover, this protocol may be used as a reference for other species in the Diaporthe genus. This is the first report to describe Agrobacterium-mediated transformation of D. phaseolorum as a tool for insertional mutagenesis.

The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics

Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H2S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments.

Cyanobacterial diversity in the phyllosphere of a mangrove forest

The cyanobacterial community colonizing phyllosphere in a well-preserved Brazilian mangrove ecosystem was assessed using cultivation-independent molecular approaches. Leaves of trees that occupy this environment (Rhizophora mangle, Avicennia schaueriana and Laguncularia racemosa) were collected along a transect beginning at the margin of the bay and extending upland. The results demonstrated that the phyllosphere of R.similar to mangle and L.similar to racemosa harbor similar assemblages of cyanobacteria at each point along the transect. A.similar to schaueriana, found only in the coastal portions of the transect, was colonized by assemblages with lower richness than the other trees. However, the results indicated that spatial location was a stronger driver of cyanobacterial community composition than plant species. Distinct cyanobacterial communities were observed at each location along the coast-to-upland transect. Clone library analysis allowed identification of 19 genera of cyanobacteria and demonstrated the presence of several uncultivated taxa. A predominance of sequences affiliated with the orders Nostocales and Oscillatoriales was observed, with a remarkable number of sequences similar to genera Symphyonemopsis/Brasilonema (order Nostocales). The results demonstrated that phyllosphere cyanobacteria in this mangrove forest ecosystem are influenced by environmental conditions as the primary driver at the ecosystem scale, with tree species exerting some effect on community structure at the local scale.

INTERSPECIFIC VARIATION OF THE BACTERIAL COMMUNITY STRUCTURE IN THE PHYLLOSPHERE OF THE THREE MAJOR PLANT COMPONENTS OF MANGROVE FORESTS

Mangrove forests encompass a group of trees species that inhabit the intertidal zones, where soil is characterized by the high salinity and low availability of oxygen. The phyllosphere of these trees represent the habitat provided on the aboveground parts of plants, supporting in a global scale, a large and complex microbial community. The structure of phyllosphere communities reflects immigration, survival and growth of microbial colonizers, which is influenced by numerous environmental factors in addition to leaf physical and chemical properties. Here, a combination of culture-base methods with PCR-DGGE was applied to test whether local or plant specific factors shape the bacterial community of the phyllosphere from three plant species (Avicenia shaueriana, Laguncularia racemosa and Rhizophora mangle), found in two mangroves. The number of bacteria in the phyllosphere of these plants varied between 3.62 x 10(4) in A. schaeriana and 6.26 x 10(3) in R. mangle. The results obtained by PCR-DGGE and isolation approaches were congruent and demonstrated that each plant species harbor specific bacterial communities in their leaves surfaces. Moreover, the ordination of environmental factors (mangrove and plant species), by redundancy analysis (RDA), also indicated that the selection exerted by plant species is higher than mangrove location on bacterial communities at phyllosphere.

Long-term effects of oil pollution in mangrove forests (Baixada Santista, Southeast Brazil) detected using a GIS-based multitemporal analysis of aerial photographs

Oil spills are potential threats to the integrity of highly productive coastal wetlands, such as mangrove forests. In October 1983, a mangrove area of nearly 300 ha located on the southeastern coast of Brazil was impacted by a 3.5 million liter crude oil spill released by a broken pipeline. In order to assess the long-term effects of oil pollution on mangrove vegetation, we carried out a GIS-based multitemporal analysis of aerial photographs of the years 1962, 1994, 2000 and 2003. Photointerpretation, visual classification, class quantification, ground-truth and vegetation structure data were combined to evaluate the oil impact. Before the spill, the mangroves exhibited a homogeneous canopy and well-developed stands. More than ten years after the spill, the mangrove vegetation exhibited three distinct zones reflecting the long-term effects of the oil pollution. The most impacted zone (10.5 ha) presented dead trees, exposed substrate and recovering stands with reduced structural development. We suggest that the distinct impact and recovery zones reflect the spatial variability of oil removal rates in the mangrove forest. This study identifies the multitemporal analysis of aerial photographs as a useful tool for assessing a system's capacity for recovery and monitoring the long-term residual effects of pollutants on vegetation dynamics, thus giving support to mangrove forest management and conservation.

Abundance and Genetic Diversity of nifH Gene Sequences in Anthropogenically Affected Brazilian Mangrove Sediments

Although mangroves represent ecosystems of global importance, the genetic diversity and abundance of functional genes that are key to their functioning scarcely have been explored. Here, we present a survey based on the nifH gene across transects of sediments of two mangrove systems located along the coast line of Sao Paulo state (Brazil) which differed by degree of disturbance, i.e., an oil-spill-affected and an unaffected mangrove. The diazotrophic communities were assessed by denaturing gradient gel electrophoresis (DGGE), quantitative PCR (qPCR), and clone libraries. The nifH gene abundance was similar across the two mangrove sediment systems, as evidenced by qPCR. However, the nifH-based PCR-DGGE profiles revealed clear differences between the mangroves. Moreover, shifts in the nifH gene diversities were noted along the land-sea transect within the previously oiled mangrove. The nifH gene diversity depicted the presence of nitrogen-fixing bacteria affiliated with a wide range of taxa, encompassing members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and also a group of anaerobic sulfate-reducing bacteria. We also detected a unique mangrove-specific cluster of sequences denoted Mgv-nifH. Our results indicate that nitrogen-fixing bacterial guilds can be partially endemic to mangroves, and these communities are modulated by oil contamination, which has important implications for conservation strategies.

The Selection Exerted by Oil Contamination on Mangrove Fungal Communities

Mangrove ecosystems are tropical environments that are characterized by the interaction between the land and the sea. As such, this ecosystem is vulnerable to oil spills. Here, we show a culture-independent survey of fungal communities that are found in the sediments of the following two mangroves that are located on the coast of Sao Paulo State (Brazil): (1) an oil-spill-affected mangrove and (2) a nearby unaffected mangrove. Samples were collected from each mangrove forest at three distinct locations (transect from sea to land), and the samples were analyzed by quantitative PCR and internal transcribed spacer (ITS)-based PCR-DGGE analysis. The abundance of fungi was found to be higher in the oil-affected mangrove. Visual observation and correspondence analysis (CA) of the ITS-based PCR-DGGE profiles revealed differences in the fungal communities between the sampled areas. Remarkably, the oil-spilled area was quite distinct from the unaffected sampling areas. On the basis of the ITS sequences, fungi that are associated with the Basidiomycota and Ascomycota taxa were most common and belonged primarily to the genera Epicoccum, Nigrospora, and Cladosporium. Moreover, the Nigrospora fungal species were shown to be sensitive to oil, whereas a group that was described as "uncultured Basidiomycota" was found more frequently in oil-contaminated areas. Our results showed an increase in fungal abundance in the oil-polluted mangrove regions, and these data indicated potential fungal candidates for remediation of the oil-affected mangroves.

Shifts in phylogenetic diversity of archaeal communities in mangrove sediments at different sites and depths in southeastern Brazil

This study focused on the structure and composition of archaeal communities in sediments of tropical mangroves in order to obtain sufficient insight into two Brazilian sites from different locations (one pristine and another located in an urban area) and at different depth levels from the surface. Terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene fragments was used to scan the archaeal community structure, and 16S rRNA gene clone libraries were used to determine the community composition. Redundancy analysis of T-RFLP patterns revealed differences in archaeal community structure according to location, depth and soil attributes. Parameters such as pH, organic matter, potassium and magnesium presented significant correlation with general community structure. Furthermore, phylogenetic analysis revealed a community composition distributed differently according to depth where, in shallow samples, 74.3% of sequences were affiliated with Euryarchaeota and 25.7% were shared between Crenarchaeota and Thaumarchaeota, while for the deeper samples, 24.3% of the sequences were affiliated with Euryarchaeota and 75.7% with Crenarchaeota and Thaumarchaeota. Archaeal diversity measurements based on 16S rRNA gene clone libraries decreased with increasing depth and there was a greater difference between depths (<18% of sequences shared) than sites (>25% of sequences shared). Taken together, our findings indicate that mangrove ecosystems support a diverse archaeal community; it might possibly be involved in nutrient cycles and are affected by sediment properties, depth and distinct locations. (C) 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Interspecific variation of the bacterial community structure in the phyllosphere of the three major plant components of mangrove forests

Mangrove forests encompass a group of trees species that inhabit the intertidal zones, where soil is characterized by the high salinity and low availability of oxygen. The phyllosphere of these trees represent the habitat provided on the aboveground parts of plants, supporting in a global scale, a large and complex microbial community. The structure of phyllosphere communities reflects immigration, survival and growth of microbial colonizers, which is influenced by numerous environmental factors in addition to leaf physical and chemical properties. Here, a combination of culture-base methods with PCR-DGGE was applied to test whether local or plant specific factors shape the bacterial community of the phyllosphere from three plant species (Avicenia shaueriana, Laguncularia racemosa and Rhizophora mangle), found in two mangroves. The number of bacteria in the phyllosphere of these plants varied between 3.62 x 10(4) in A. schaeriana and 6.26 x 10³ in R. mangle. The results obtained by PCR-DGGE and isolation approaches were congruent and demonstrated that each plant species harbor specific bacterial communities in their leaves surfaces. Moreover, the ordination of environmental factors (mangrove and plant species), by redundancy analysis (RDA), also indicated that the selection exerted by plant species is higher than mangrove location on bacterial communities at phyllosphere.

Long-term effects of oil pollution in mangrove forests (Baixada Santista, Southeast Brazil) detected using a GIS-based multitemporal analysis of aerial photographs

Oil spills are potential threats to the integrity of highly productive coastal wetlands, such as mangrove forests. In October 1983, a mangrove area of nearly 300 ha located on the southeastern coast of Brazil was impacted by a 3.5 million liter crude oil spill released by a broken pipeline. In order to assess the long-term effects of oil pollution on mangrove vegetation, we carried out a GIS-based multitemporal analysis of aerial photographs of the years 1962, 1994, 2000 and 2003. Photointerpretation, visual classification, class quantification, ground-truth and vegetation structure data were combined to evaluate the oil impact. Before the spill, the mangroves exhibited a homogeneous canopy and well-developed stands. More than ten years after the spill, the mangrove vegetation exhibited three distinct zones reflecting the long-term effects of the oil pollution. The most impacted zone (10.5 ha) presented dead trees, exposed substrate and recovering stands with reduced structural development. We suggest that the distinct impact and recovery zones reflect the spatial variability of oil removal rates in the mangrove forest. This study identifies the multitemporal analysis of aerial photographs as a useful tool for assessing a system's capacity for recovery and monitoring the long-term residual effects of pollutants on vegetation dynamics, thus giving support to mangrove forest management and conservation.

Isotopes Trace Biogeochemistry and Sources of Cu and Zn in an intertidal soil

River floodplain soils are sinks and potential sources for toxic trace metals like Cu and Zn. We hypothesize that stable Cu and Zn isotope ratios reflect both the mobilization and the sources of metals. We determined the soil properties, the concentrations and partitioning of Cu and Zn, and variations in δ65Cu and δ66Zn values in a core obtained from an Aquic Udifluvent developed on a freshwater intertidal mudflat of the River Elbe, Germany. The core was sampled at 2 cm intervals to a depth of 34 cm, which corresponds to approximately 9 yr of sedimentation. Elevated concentrations of Cu (up to 320 μg g−1) and Zn (up to 2080 μg g−1) indicated anthropogenic pollution. At the time of sampling the redox conditions changed from oxic (Eh 200 to 400 mV, above 22 cm deep) to strongly anoxic conditions (-100 to -200 mV, below 22 cm deep). The δ65Cu values varied systematically with depth (from -0.02 to 0.16‰) and were correlated with the Fe, C, and N concentrations. Although pre-depositional variations cannot be ruled out, the systematic variation with depth suggests post-sedimentation fractionation of δ65Cu in response to seasonally variable organic matter deposition and redox conditions. In contrast, the δ66ZnIRMM values were uniform (from -0.07 to 0.01‰) throughout the core, indicating that the Zn isotopes did not significantly fractionate after deposition and that the Zn sources were homogeneous throughout the sedimentation.

Time of emergence of trends in ocean biogeochemistry

For the detection of climate change, not only the magnitude of a trend signal is of significance. An essential issue is the time period required by the trend to be detectable in the first place. An illustrative measure for this is time of emergence (ToE), that is, the point in time when a signal finally emerges from the background noise of natural variability. We investigate the ToE of trend signals in different biogeochemical and physical surface variables utilizing a multi-model ensemble comprising simulations of 17 Earth system models (ESMs). We find that signals in ocean biogeochemical variables emerge on much shorter timescales than the physical variable sea surface temperature (SST). The ToE patterns of pCO2 and pH are spatially very similar to DIC (dissolved inorganic carbon), yet the trends emerge much faster – after roughly 12 yr for the majority of the global ocean area, compared to between 10 and 30 yr for DIC. ToE of 45–90 yr are even larger for SST. In general, the background noise is of higher importance in determining ToE than the strength of the trend signal. In areas with high natural variability, even strong trends both in the physical climate and carbon cycle system are masked by variability over decadal timescales. In contrast to the trend, natural variability is affected by the seasonal cycle. This has important implications for observations, since it implies that intra-annual variability could question the representativeness of irregularly sampled seasonal measurements for the entire year and, thus, the interpretation of observed trends.