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.

Factors controlling water-column respiration in rivers of the central and southwestern Amazon Basin

We examined the factors controlling the variability in water-column respiration rates in Amazonian rivers. Our objectives were to determine the relationship between respiration rates and the in situ concentrations of the size classes of organic carbon (OC), and the biological source (C-3 and C-4 plants and phytoplankton) of organic matter (OM) supporting respiration. Respiration was measured along with OC size fractions and dissolved oxygen isotopes (delta O-18-O-2) in rivers of the central and southwestern Amazon Basin. Rates ranged from 0.034 mu mol O-2 L-1 h(-1) to 1.78 mu mol O-2 L-1 h(-1), and were four-fold higher in rivers with evidence of photosynthetic production (demonstrated by delta O-18-O-2<24.2 parts per thousand) as compared to rivers lacking such evidence (delta O-18-O-2>24.2 parts per thousand; 1.35 +/- 0.22 vs. 0.30 +/- 0.29 mu mol L-1 h(-1)). Rates were likely elevated in the former rivers, which were all sampled during low water, due to the stimulation of heterotrophic respiration via the supply of a labile, algal-derived substrate and/or the occurrence of autotrophic respiration. The organic composition of fine particulate OM (FPOM) of these rivers is consistent with a phytoplankton origin. Multiple linear regression analysis indicates that [FPOC], C:N-FPOC ratios, and [O-2] account for a high amount of the variability in respiration rates (r(2) = 0.80). Accordingly, FPOC derived from algal sources is associated with elevated respiration rates. The delta C-13 of respiration-derived CO2 indicates that the role of phytoplankton, C-3 plants, and C-4 grasses in supporting respiration is temporally and spatially variable. Future scaling work is needed to evaluate the significance of phytoplankton production to basin-wide carbon cycling.

Warming alters photosynthetic rates of sub-boreal peatland vegetation

Boreal peatlands are important in the global carbon cycle. Despite covering only 3% of the global land area, peatlands store approximately one third of all soil carbon. Temperature is one of the major drivers in peatland carbon cycling as it affects both plant production and CO2 fluxes from soils. However, it is relatively unknown how boreal peatland plant photosynthesis is affected by higher temperatures. Therefore, we measured plant photosynthetic rates under two different warming treatments in a poor fen in Northern Michigan. Eighteen plots were established that were divided into three treatments: control, open-top chamber (OTC) warming and infrared (IR) lamp warming. Previous work at this site has shown that there was a significant increase in canopy and peat temperature with IR warming (5°C and 1.4°C respectively), while the OTC’s had mixed overall warming. Plots were divided equally into lawns and hummocks. We measured mid-day carbon dioxide (CO2) uptake on sedges (Carex utriculata), shrubs (Chamaedaphne calyculata) and Sphagnum mosses. Sphagnum moss net primary production (NPP) was also measured with cranked wires and compared with CO2 uptake. Our results indicate that there was no significant difference in sedge CO2 uptake, while shrub CO2 uptake significantly decreased with warming. A significant increase occurred in Sphagnum moss gross ecosystem production (GEP), ecosystem respiration (ER) and net ecosystem exchange (NEE). Contrary to the positive CO2 exchange of Sphagnum, overall NPP decreased significantly in hummocks with both warming treatments. The results of the study indicate that temperature partly limits the photosynthetic capacity of plants in sub-boreal peatlands, but not all species respond similarly to higher temperatures.

BEYOND ROOTS ALONE: NOVEL METHODOLOGIES FOR ANALYZING COMPLEX SOIL AND MINIRHIZOTRON IMAGERY USING IMAGE PROCESSING AND GIS TOOLS

Quantifying belowground dynamics is critical to our understanding of plant and ecosystem function and belowground carbon cycling, yet currently available tools for complex belowground image analyses are insufficient. We introduce novel techniques combining digital image processing tools and geographic information systems (GIS) analysis to permit semi-automated analysis of complex root and soil dynamics. We illustrate methodologies with imagery from microcosms, minirhizotrons, and a rhizotron, in upland and peatland soils. We provide guidelines for correct image capture, a method that automatically stitches together numerous minirhizotron images into one seamless image, and image analysis using image segmentation and classification in SPRING or change analysis in ArcMap. These methods facilitate spatial and temporal root and soil interaction studies, providing a framework to expand a more comprehensive understanding of belowground dynamics.

Unraveling environmental drivers of a recent increase in Swiss fungi fruiting

Disentangling biotic and abiotic drivers of wild mushroom fruiting is fraught with difficulties because mycelial growth is hidden belowground, symbiotic and saprotrophic supply strategies may interact, and myco-ecological observations are often either discontinuous or too short. Here, we compiled and analyzed 115 417 weekly fungal fruit body counts from permanent Swiss inventories between 1975 and 2006. Mushroom fruiting exhibited an average autumnal delay of 12 days after 1991 compared with before, the annual number of fruit bodies increased from 1801 to 5414 and the mean species richness doubled from 10 to 20. Intra- and interannual coherency of symbiotic and saprotrophic mushroom fruiting, together with little agreement between mycorrhizal yield and tree growth suggests direct climate controls on fruit body formation of both nutritional modes. Our results contradict a previously reported declining of mushroom harvests and propose rethinking the conceptual role of symbiotic pathways in fungi-host interaction. Moreover, this conceptual advancement may foster new cross-disciplinary research avenues, and stimulate questions about possible amplifications of the global carbon cycle, as enhanced fungal production in moist mid-latitude forests rises carbon cycling and thus increases greenhouse gas exchanges between terrestrial ecosystems and the atmosphere.

Oceanography during TYDEMAN cruise DCM (DeepChlorMax) to the Equatorial Atlantic

The cruise with RV Tydeman was devoted to study permanently stratified plankton systems in the (sub)tropical ocean, which are characterised by a deep chlorophyll peak between 80 and 150 m. To minimise lateral effects by horizontal transport of nutrients and organic matter from river outflow and upwelling regions, stations were selected in the middle of the North Atlantic Ocean between the continents of America and Africa. (5 - 35° N and 50 - 15° W). Here the vertical distributions of light and nutrients control the abundance and growth of autotrophic algae in the thermically stratified water column. This phytoplankton is numerically dominated by the prokaryotic picoplankters Synechococcus spp. and Prochlorococcus spp., which are smaller than 2 ?m. The productivity of the 100 to 150 m deep euphotic zone can be high, because a high heterotrophic/autotrophic biomass ratio induces a rapid regeneration of nutrients and inorganic carbon. Primary grazers are mainly micro-organisms such as heterotrophic nannoflagellates and ciliates, which feed on the small algae and on bacteria. Heterotrophic bacteria can outnumber the autotrophic algae, because their number is related to the substrate pools of dissolved and particulate dead organic matter. These DOC and detritus pools reach equilibrium at a concentration, where the rate of their production (proportional to algal biomass) equals their mineralisation and sinking rate (proportional to the concentration and weight of POC and detritus). At a relatively low value of the weight-specific loss rates, the equilibrium concentration of these carbon pools and their load of bacteria can be high. The bacterial productivity is proportional to the mineralisation rate, which in a steady state can never be higher than the rate of primary production. Hence the ratio in turnover rate of bacteria and autotrophs tends to be reciprocally proportional to their biomass ratio.

Age models of sediment cores from the Southern Ocean

Recent geochemical models invoke ocean alkalinity changes, particularly in the surface Southern Ocean, to explain glacial age pCO2 reduction. In such models, alkalinity increases in glacial periods are driven by reductions in North Atlantic Deep Water (NADW) supply, which lead to increases in deep-water nutrients and dissolution of carbonate sediments, and to increased alkalinity of Circumpolar Deep Water upwelling in the surface Southern Ocean. We use cores from the Southeast Indian Ridge and from the deep Cape Basin in the South Atlantic to show that carbonate dissolution was enhanced during glacial stages in areas now bathed by Circumpolar Deep Water. This suggests that deep Southern Ocean carbonate ion concentrations were lower in glacial stages than in interglacials, rather than higher as suggested by the polar alkalinity model [Broecker and Peng, 1989, doi:10.1029/GB001i001p00015]. Our observations show that changes in Southern Ocean CaCO3 preservation are coherent with changes in the relative flux of NADW, suggesting that Southern Ocean carbonate chemistry is closely linked to changes in deepwater circulation. The pattern of enhanced dissolution in glacials is consistent with a reduction in the supply of nutrient-depleted water (NADW) to the Southern Ocean and with an increase of nutrients in deep water masses. Carbonate mass accumulation rates on the Southeast Indian Ridge (3200-3800 m), and in relatively shallow cores (<3000 m) from the Kerguelen Plateau and the South Pacific were significantly reduced during glacial stages, by about 50%. The reduced carbonate mass accumulation rates and enhanced dissolution during glacials may be partly due to decreases in CaCO3:Corg flux ratios, acting as another mechanism which would raise the alkalinity of Southern Ocean surface waters. The polar alkalinity model assumes that the ratio of organic carbon to carbonate production on surface alkalinity is constant. Even if overall productivity in the Southern Ocean were held constant, a decrease in the CaCO3:Corg ratio would result in increased alkalinity and reduced pCO2 in Southern Ocean surface waters during glacials. This ecologically driven surface alkalinity change may enhance deepwater-mediated changes in alkalinity, and amplify rapid changes in pCO2.

Paleomegnetic and geochemistry of sediments from the early Aptian Oceanic Anoxic Event

The early Aptian Oceanic Anoxic Event (OAE1a, 120 Ma) represents a geologically brief time interval in the mid-Cretaceous greenhouse world that is characterized by increased organic carbon accumulation in marine sediments, sudden biotic changes, and abrupt carbon-isotope excursions indicative of significant perturbations to global carbon cycling. The brevity of these drastic environmental changes (< 10**6 year) and the typically 10**6 year temporal resolution of the available chronologies, however, represent a critical gap in our knowledge of OAE1a. We have conducted a high-resolution investigation of three widely distributed sections, including the Cismon APTICORE in Italy, Santa Rosa Canyon in northeastern Mexico, and Deep Sea Drilling Project (DSDP) Site 398 off the Iberian margin in the North Atlantic Ocean, which represent a range of depositional environments where condensed and moderately expanded OAE1a intervals are recorded. The objectives of this study are to establish orbital chronologies for these sections and to construct a common, high-resolution timescale for OAE1a. Spectral analyses of the closely-spaced (corresponding to ~5 to 10 kyr) measurements of calcium carbonate content of the APTICORE, magnetic susceptibility (MS) and anhysteretic remanent magnetization (ARM) of the Santa Rosa samples, and MS, ARM and ARM/IRM, where IRM is isothermal remanent magnetization, of Site 398 samples reveal statistically significant cycles. These cycles exhibit periodicity ratios and modulation patterns similar to those of the mid-Cretaceous orbital cycles, suggesting that orbital variations may have modulated depositional processes. Orbital control allows us to estimate the duration of unique, globally identifiable stages of OAE1a. Although OAE1a had a duration of ~1.0 to 1.3 Myr, the initial perturbation represented by the negative carbon-isotope excursion was rapid, lasting for ~27-44 kyr. This estimate could serve as a basis for constraining triggering mechanisms for OAE1a.

(Data S1) Palynological analysis of IODP and ODP sediment cores around the Antarctic margin

The circum-Antarctic Southern Ocean is an important region for global marine food webs and carbon cycling because of sea-ice formation and its unique plankton ecosystem. However, the mechanisms underlying the installation of this distinct ecosystem and the geological timing of its development remain unknown. Here, we show, on the basis of fossil marine dinoflagellate cyst records, that a major restructuring of the Southern Ocean plankton ecosystem occurred abruptly and concomitant with the first major Antarctic glaciation in the earliest Oligocene (~33.6 million years ago). This turnover marks a regime shift in zooplankton-phytoplankton interactions and community structure, which indicates the appearance of eutrophic and seasonally productive environments on the Antarctic margin. We conclude that earliest Oligocene cooling, ice-sheet expansion, and subsequent sea-ice formation were important drivers of biotic evolution in the Southern Ocean.

Oxygen contents, sulfate concentrations, and changes of IPLs under different storage conditions of samples from ODP Leg 204 and IODP Expedition 311

We have studied the effects of slow infiltration of oxygen on microbial communities in refrigerated legacy samples from ocean drilling expeditions. Storage was in heat-sealed, laminated foil bags with a N2 headspace for geomicrobiological studies. Analysis of microbial lipids suggests that Bacteria were barely detectable in situ but increased remarkably during storage. Detailed molecular examination of a methane-rich sediment horizon showed that refrigeration triggered selective growth of ANME-2 archaea and a drastic change in the bacterial community. Subsequent enrichment targeting methanogens yielded exclusively methylotrophs, which were probably selected for by high sulfate levels caused by oxidation of reduced sulfur species. We provide recommendations for sample storage in future ocean drilling expeditions.

Methanol and ethanol analysis in marine sediment pore water

Low-molecular-weight (LMW) alcohols are produced during the microbial degradation of organic matter from precursors such as lignin, pectin, and carbohydrates. The biogeochemical behavior of these alcohols in marine sediment is poorly constrained but potentially central to carbon cycling. Little is known about LMW alcohols in sediment pore waters because of their low concentrations and high water miscibility, both of which pose substantial analytical challenges. In this study, three alternative methods were adapted for the analysis of trace amounts of methanol and ethanol in small volumes of saline pore waters: direct aqueous injection (DAI), solid-phase microextraction (SPME), and purge and trap (P&T) in combination with gas chromatography (GC) coupled to either a flame ionization detector (FID) or a mass spectrometer (MS). Key modifications included the desalination of samples prior to DAI, the use of a threaded midget bubbler to purge small-volume samples under heated conditions and the addition of salt during P&T. All three methods were validated for LMW alcohol analysis, and the lowest detection limit (60 nM and 40 nM for methanol and ethanol, respectively) was achieved with the P&T technique. With these methods, ambient concentrations of volatile alcohols were determined for the first time in marine sediment pore waters of the Black Sea and the Gulf of Mexico. A strong correlation between the two compounds was observed and tentatively interpreted as being controlled by similar sources and sinks at the examined stations.

Benthic stable-isotope records of ODP Site 208-1262, South Atlantic

The Late Paleocene and Early Eocene were characterised by warm greenhouse climates, punctuated by a series of rapid warming and ocean acidification events known as "hyperthermals", thought to have been paced or triggered by orbital cycles. While these hyperthermals, such as the Paleocene Eocene Thermal Maximum (PETM), have been studied in great detail, the background low-amplitude cycles seen in carbon and oxygen-isotope records throughout the Paleocene-Eocene have hitherto not been resolved. Here we present a 7.7 million year (myr) long, high-resolution, orbitally-tuned, benthic foraminiferal stable-isotope record spanning the late Paleocene and early Eocene interval (~52.5 - 60.5 Ma) from Ocean Drilling Program (ODP) Site 1262, South Atlantic. This high resolution (~2-4 kyr) record allows the changing character and phasing of orbitally-modulated cycles to be studied in unprecedented detail as it reflects the long-term trend in carbon cycle and climate over this interval. The main pacemaker in the benthic oxygen-isotope (d18O) and carbon-isotope (d13C) records from ODP Site 1262, are the long (405 kyr) and short (100 kyr) eccentricity cycles, and precession (21 kyr). Obliquity (41 kyr) is almost absent throughout the section except for a few brief intervals where it has a relatively weak influence. During the course of the Early Paleogene record, and particularly in the latest Paleocene, eccentricity-paced negative carbon-isotope excursions (d13C, CIEs) and coeval negative oxygen-isotope (d18O) excursions correspond to low carbonate (CaCO3) and coarse fraction (%CF) values due to increased carbonate dissolution, suggesting shoaling of the lysocline and accompanied changes in the global exogenic carbon cycle. These negative CIEs and d18O events coincide with maxima in eccentricity, with changes in d18O leading changes in d13C by ~6 (±5) kyr in the 405-kyr band and by ~3 (±1) kyr in the higher frequency 100-kyr band on average. However, these phase lags are not constant, with the lag in the 405-kyr band extending from ~4 (±5) kyr to ~21 (±2) kyr from the late Paleocene to the early Eocene, suggesting a progressively weaker coupling of climate and the carbon-cycle with time. The higher amplitude 405-kyr cycles in the latest Paleocene are associated with changes in bottom water temperature of 2-4ºC, while the most prominent 100 kyr-paced cycles can be accompanied by changes of up to 1.5ºC. Comparison of the 1262 record with a lower resolution, but orbitally-tuned benthic record for Site 1209 in the Pacific allows for verification of key features of the benthic isotope records which are global in scale including a key warming step at 57.7 Ma.