Food web complexity weakens size-based constraints on the pyramids of life.

Marine ecosystems are generally expected to have bottom-heavy trophic structure (more plants than animals) due to size-based constraints arising from increased metabolic requirements and inefficient energy transfer. However, size-based (allometric) approaches are often limited to confined trophic-level windows where energy transfer is predicted by size alone and are constrained to a balance between bottom-up and top-down control at steady state. In real food webs, energy flow is more complex and imbalances in top-down and bottom-up processes can also shape trophic structure. We expand the size-based theory to account for complex food webs and show that moderate levels of food web connectance allow for inverted trophic structure more often than predicted, especially in marine ecosystems. Trophic structure inversion occurs due to the incorporation of complex energy pathways and top-down effects on ecosystems. Our results suggest that marine ecosystems should be top-heavy, and observed bottom-heavy trophic structure may be a result of human defaunation of the ocean that has been more extreme than presently recognized.

Microbial diversity and activity in seafloor brine lake sediments (Alaminos Canyon block 601, Gulf of Mexico).

The microbial communities thriving in deep-sea brines are sustained largely by energy rich substrates supplied through active seepage. Geochemical, microbial activity, and microbial community composition data from different habitats at a Gulf of Mexico brine lake in Alaminos Canyon revealed habitat-linked variability in geochemistry that in turn drove patterns in microbial community composition and activity. The bottom of the brine lake was the most geochemically extreme (highest salinity and nutrient concentrations) habitat and its microbial community exhibited the highest diversity and richness indices. The habitat at the upper halocline of the lake hosted the highest rates of sulfate reduction and methane oxidation, and the largest inventories of dissolved inorganic carbon, particulate organic carbon, and hydrogen sulfide. Statistical analyses indicated a significant positive correlation between the bacterial and archaeal diversity in the bottom brine sample and NH4+ inventories. Other environmental factors with positive correlation with microbial diversity indices were DOC, H2 S, and DIC concentrations. The geochemical regime of different sites within this deep seafloor extreme environment exerts a clear selective force on microbial communities and on patterns of microbial activity.

Barite encrustation of benthic sulfur-oxidizing bacteria at a marine cold seep.

Crusts and chimneys composed of authigenic barite are found at methane seeps and hydrothermal vents that expel fluids rich in barium. Microbial processes have not previously been associated with barite precipitation in marine cold seep settings. Here, we report on the precipitation of barite on filaments of sulfide-oxidizing bacteria at a brine seep in the Gulf of Mexico. Barite-mineralized bacterial filaments in the interiors of authigenic barite crusts resemble filamentous sulfide-oxidizing bacteria of the genus Beggiatoa. Clone library and iTag amplicon sequencing of the 16S rRNA gene show that the barite crusts that host these filaments also preserve DNA of Candidatus Maribeggiatoa, as well as sulfate-reducing bacteria. Isotopic analyses show that the sulfur and oxygen isotope compositions of barite have lower δ(34)S and δ(18)O values than many other marine barite crusts, which is consistent with barite precipitation in an environment in which sulfide oxidation was occurring. Laboratory experiments employing isolates of sulfide-oxidizing bacteria from Gulf of Mexico seep sediments showed that under low sulfate conditions, such as those encountered in brine fluids, sulfate generated by sulfide-oxidizing bacteria fosters rapid barite precipitation localized on cell biomass, leading to the encrustation of bacteria in a manner reminiscent of our observations of barite-mineralized Beggiatoa in the Gulf of Mexico. The precipitation of barite directly on filaments of sulfide-oxidizing bacteria, and not on other benthic substrates, suggests that sulfide oxidation plays a role in barite formation at certain marine brine seeps where sulfide is oxidized to sulfate in contact with barium-rich fluids, either prior to, or during, the mixing of those fluids with sulfate-containing seawater in the vicinity of the sediment/water interface. As with many other geochemical interfaces that foster mineral precipitation, both biological and abiological processes likely contribute to the precipitation of barite at marine brine seeps such as the one studied here.

High rates of anaerobic methane oxidation in freshwater wetlands reduce potential atmospheric methane emissions.

The role of anaerobic oxidation of methane (AOM) in wetlands, the largest natural source of atmospheric methane, is poorly constrained. Here we report rates of microbially mediated AOM (average rate=20 nmol cm(-3) per day) in three freshwater wetlands that span multiple biogeographical provinces. The observed AOM rates rival those in marine environments. Most AOM activity may have been coupled to sulphate reduction, but other electron acceptors remain feasible. Lipid biomarkers typically associated with anaerobic methane-oxidizing archaea were more enriched in (13)C than those characteristic of marine systems, potentially due to distinct microbial metabolic pathways or dilution with heterotrophic isotope signals. On the basis of this extensive data set, AOM in freshwater wetlands may consume 200 Tg methane per year, reducing their potential methane emissions by over 50%. These findings challenge precepts surrounding wetland carbon cycling and demonstrate the environmental relevance of an anaerobic methane sink in ecosystems traditionally considered strong methane sources.

Anaerobic oxidation of methane by sulfate in hypersaline groundwater of the Dead Sea aquifer.

Geochemical and microbial evidence points to anaerobic oxidation of methane (AOM) likely coupled with bacterial sulfate reduction in the hypersaline groundwater of the Dead Sea (DS) alluvial aquifer. Groundwater was sampled from nine boreholes drilled along the Arugot alluvial fan next to the DS. The groundwater samples were highly saline (up to 6300 mm chlorine), anoxic, and contained methane. A mass balance calculation demonstrates that the very low δ(13) CDIC in this groundwater is due to anaerobic methane oxidation. Sulfate depletion coincident with isotope enrichment of sulfur and oxygen isotopes in the sulfate suggests that sulfate reduction is associated with this AOM. DNA extraction and 16S amplicon sequencing were used to explore the microbial community present and were found to be microbial composition indicative of bacterial sulfate reducers associated with anaerobic methanotrophic archaea (ANME) driving AOM. The net sulfate reduction seems to be primarily controlled by the salinity and the available methane and is substantially lower as salinity increases (2.5 mm sulfate removal at 3000 mm chlorine but only 0.5 mm sulfate removal at 6300 mm chlorine). Low overall sulfur isotope fractionation observed ((34) ε = 17 ± 3.5‰) hints at high rates of sulfate reduction, as has been previously suggested for sulfate reduction coupled with methane oxidation. The new results demonstrate the presence of sulfate-driven AOM in terrestrial hypersaline systems and expand our understanding of how microbial life is sustained under the challenging conditions of an extremely hypersaline environment.

Biocomplexity in mangrove ecosystems.

Mangroves are an ecological assemblage of trees and shrubs adapted to grow in intertidal environments along tropical coasts. Despite repeated demonstration of their economic and societal value, more than 50% of the world's mangroves have been destroyed, 35% in the past two decades to aquaculture and coastal development, altered hydrology, sea-level rise, and nutrient overenrichment. Variations in the structure and function of mangrove ecosystems have generally been described solely on the basis of a hierarchical classification of the physical characteristics of the intertidal environment, including climate, geomorphology, topography, and hydrology. Here, we use the concept of emergent properties at multiple levels within a hierarchical framework to review how the interplay between specialized adaptations and extreme trait plasticity that characterizes mangroves and intertidal environments gives rise to the biocomplexity that distinguishes mangrove ecosystems. The traits that allow mangroves to tolerate variable salinity, flooding, and nutrient availability influence ecosystem processes and ultimately the services they provide. We conclude that an integrated research strategy using emergent properties in empirical and theoretical studies provides a holistic approach for understanding and managing mangrove ecosystems.

Molecular analysis of the sulfate reducing and archaeal community in a meromictic soda lake (Mono Lake, California) by targeting 16S rRNA, mcrA, apsA, and dsrAB genes.

Sulfate reduction is the most important process involved in the mineralization of carbon in the anoxic bottom waters of Mono Lake, an alkaline, hypersaline, meromictic Lake in California. Another important biogeochemical process in Mono Lake is thought to be sulfate-dependent methane oxidation (SDMO). However little is known about what types of organisms are involved in these processes in Mono Lake. Therefore, the sulfate-reducing and archaeal microbial community in Mono Lake was analyzed by targeting 16S rRNA, methyl-coenzyme M reductase (mcrA), adenosine-5'-phosphosulfate (apsA), and dissimilatory sulfite reductase (dsrAB) genes to investigate the sulfate-reducing and archaeal community with depth. Most of the 16S rRNA gene sequences retrieved from the samples fell into the delta-subdivision of the Proteobacteria. Phylogenetic analyses suggested that the clones obtained represented sulfate-reducing bacteria, which are probably involved in the mineralization of carbon in Mono Lake, many of them belonging to a novel line of descent in the delta-Proteobacteria. Only 6% of the sequences retrieved from the samples affiliated to the domain Euryarchaeota but did not represent Archaea, which is considered to be responsible for SDMO [Orphan et al. 2001: Appl Environ Microbiol 67:1922-1934; Teske et al.: Appl Environ Microbiol 68:1994-2007]. On the basis of our results and thermodynamic arguments, we proposed that SDMO in hypersaline environments is presumably carried out by SRB alone. Polymerase chain reaction (PCR) amplifications of the mcrA-, apsA-, and dsrAB genes in Mono Lake samples were, in most cases, not successful. Only the PCR amplification of the apsA gene was partially successful. The amplification of these functional genes was not successful because there was either insufficient "target" DNA in the samples, or the microorganisms in Mono Lake have divergent functional genes.

Analysis of ammonia-oxidizing bacteria from hypersaline Mono Lake, California, on the basis of 16S rRNA sequences.

Ammonia-oxidizing bacteria were detected by PCR amplification of DNA extracted from filtered water samples throughout the water column of Mono Lake, California. Ammonia-oxidizing members of the beta subdivision of the division Proteobacteria (beta-subdivision Proteobacteria) were detected using previously characterized PCR primers; target sequences were detected by direct amplification in both surface water and below the chemocline. Denaturing gradient gel electrophoresis analysis indicated the presence of at least four different beta-subdivision ammonia oxidizers in some samples. Subsequent sequencing of amplified 16S rDNA fragments verified the presence of sequences very similar to those of cultured Nitrosomonas strains. Two separate analyses, carried out under different conditions (different reagents, locations, PCR machines, sequencers, etc.), 2 years apart, detected similar ranges of sequence diversity in these samples. It seems likely that the physiological diversity of nitrifiers exceeds the diversity of their ribosomal sequences and that these sequences represent members of the Nitrosomonas europaea group that are acclimated to alkaline, high-salinity environments. Primers specific for Nitrosococcus oceanus, a marine ammonia-oxidizing bacterium in the gamma subdivision of the Proteobacteria, did not amplify target from any samples.

Microscale characterization of dissolved organic matter production and uptake in marine microbial mat communities.

Intertidal marine microbial mats exhibited biologically mediated uptake of low molecular weight dissolved organic matter (DOM), including D-glucose, acetate, and an L-amino acid mixture at trace concentrations. Uptake of all compounds occurred in darkness, but was frequently enhanced under natural illumination. The photosystem 2 inhibitor, 3-(3,4-dichlorophenyl)-1,1-dimethyl urea (DCMU) generally failed to inhibit light-stimulated DOM uptake. Occasionally, light plus DCMU-amended treatments led to uptake rates higher than light-incubated samples, possibly due to phototrophic bacteria present in subsurface anoxic layers. Uptake was similar with either 3H- or 14C-labeled substrates, indicating that recycling of labeled CO2 via photosynthetic fixation was not interfering with measurements of light-stimulated DOM uptake. Microautoradiographs showed a variety of pigmented and nonpigmented bacteria and, to a lesser extent, cyanobacteria and eucaryotic microalgae involved in light-mediated DOM uptake. Light-stimulated DOM uptake was often observed in bacteria associated with sheaths and mucilage surrounding filamentous cyanobacteria, revealing a close association of organisms taking up DOM with photoautotrophic members of the mat community. The capacity for dark- and light-mediated heterotrophy, coupled to efficient retention of fixed carbon in the mat community, may help optimize net production and accretion of mats, even in oligotrophic waters.