Sediment microbial communities at CO2 seeps in Papua New Guinea

To understand how ocean acidification (OA) influences sediment microbial communities, naturally CO2-rich sites are increasingly being used as OA analogues. However, the characterization of these naturally CO2-rich sites is often limited to OA-related variables, neglecting additional environmental variables that may confound OA effects. Here, we used an extensive array of sediment and bottom water parameters to evaluate pH effects on sediment microbial communities at hydrothermal CO2 seeps in Papua New Guinea. The geochemical composition of the sediment pore water showed variations in the hydrothermal signature at seep sites with comparable pH, allowing the identification of sites that may better represent future OA scenarios. At these sites, we detected a 60% shift in the microbial community composition compared with reference sites, mostly related to increases in Chloroflexi sequences. pH was among the factors significantly, yet not mainly, explaining changes in microbial community composition. pH variation may therefore often not be the primary cause of microbial changes when sampling is done along complex environmental gradients. Thus, we recommend an ecosystem approach when assessing OA effects on sediment microbial communities under natural conditions. This will enable a more reliable quantification of OA effects via a reduction of potential confounding effects. This pangaea entry contains the data on the microbial community structure and bottom water parameters.

Pigments of sediment cores of the Northwest European Continental Margin

In the context of the European OMEX Programme this investigation focused on gradients in the biomass and activity of the small benthic size spectrum along a transect across the Goban Spur from the outer Celtic Sea into Porcupine Abyssal Plain. The effects of food pulses (seasonal, episodic) on this part of the benthic size spectrum were investigated. Sediments sampled during eight expeditions at different seasons covering a range from 200 m to 4800 m water depth were assayed with biochemical bulk measurements: determinations of chloroplastic pigment equivalents (CPE), the sum of chlorophyll a and its breakdown products, provide information concerning the input of phytodetrital matter to the seafloor; phospholipids were analyzed to estimate the total biomass of small benthic organisms (including bacteria, fungi, flagellata, protozoa and small metazoan meiofauna). A new term 'small size class biomass' (SSCB) is introduced for the biomass of the smallest size classes of sediment-inhabiting organisms; the reduction of fluorescein-di-acetate (FDA) was determined to evaluate the potential activity of ester-cleaving bacterial exoenzymes in the sediment samples. At all stations benthic biomass was predominantly composed of the small size spectrum (90% on the shelf; 97-98% in the bathyal and abyssal parts of the transect). Small size class biomass (integrated over a 10 cm sediment column) ranged from 8 g C/m**2 on the shelf to 2.1 g C/m**2 on the adjacent Porcupine Abyssal Plain, exponentially decreasing with increasing water depth. However, a correlation between water depth and SSCB, macrofauna biomass as well as metazoan meiofauna biomass exhibited a significantly flatter slope for the small size classes in comparison to the larger organisms. CPE values indicated a pronounced seasonal cycle on the shelf and upper slope with twin peaks of phytodetrital deposition in mid spring and late summer. The deeper stations seem to receive a single annual flux maximum in late summer. SSCB and heterotrophic activity are significantly correlated to the amount of sediment-bound pigments. Seasonality in pigment concentrations is clearly followed by SSCB and activity. In contrast to macro- and megafauna which integrate over larger periods (months/years), the small benthic size classes, namely bacteria and foraminifera, proved to be the most reactive potential of the benthic communities to any perturbations on short time scales (days/weeks). The small size classes, therefore, occupy a key role in early diagenetic processes.

Pore water measurements of sediment cores from the Helgoland mud area, North Sea

Iron reduction in subseafloor sulfate-depleted and methane-rich marine sediments is currently a subject of interest in subsurface geomicrobiology. While iron reduction and microorganisms involved have been well studied in marine surface sediments, little is known about microorganisms responsible for iron reduction in deep methanic sediments. Here, we used quantitative PCR (Q-PCR)-based 16S rRNA gene copy numbers and pyrosequencing-based relative abundances of bacteria and archaea to investigate covariance between distinct microbial populations and specific geochemical profiles in the top 5 m of sediment cores from the Helgoland mud area, North Sea. We found that gene copy numbers of bacteria and archaea were specifically higher around the peak of dissolved iron in the methanic zone (250-350 cm. The higher copy numbers at these depths were also reflected by the relative sequence abundances of members of the candidate division JS1, methanogenic and Methanohalobium/ANME-3 related archaea. The distribution of these populations was strongly correlated to the profile of pore-water Fe2+ while that of Desulfobacteraceae corresponded to the pore-water sulfate profile. Furthermore, specific JS1 populations also strongly co-varied with the distribution of Methanosaetaceae in the methanic zone. Our data suggest that the interplay among JS1 bacteria, methanogenic archaea and Methanohalobium/ANME-3-related archaea may be important for iron reduction and methane cycling in deep methanic sediments of the Helgoland mud area and perhaps in other methane-rich depositional environments. .

Sediment Budget for Cane Land on the Lower Herbert River Floodplain, North Queensland, Australia

Land use in the river catchments of tropical North Queensland appears to have increased the export of sediment and nutrients to the coast. Although evidence of harmful effect of sediment on coastal and riverine ecosystems is limited, there is a growing concern about its possible negative impacts. Sugarcane cultivation on the floodplains of the tropical North Queensland river catchments is thought to be an important source of excess sediment in the river drainage systems. Minimum-tillage, trash blanket harvesting has been shown to reduce erosion from sloping sugarcane fields, but in the strongly modified floodplain landscape other elements (e.g. drains, water furrows and headlands) could still be important sediment sources. The main objectives of this thesis are to quantify the amount of sediment coming from low-lying cane land and identify the important sediment sources in the landscape. The results of this thesis enable sugarcane farmers to take targeted measures for further reduction of the export of sediment and nutrients. Sediment budgets provide a useful approach to identify and quantify potential sediment sources. For this study a sediment budget is calculated for a part of the Ripple Creek catchment, which is a sub-catchment of the Lower Herbert River. The input of sediment from all potential sources in cane land and the storage of sediment within the catchment have been quantified and compared with the output of sediment from the catchment. Input from, and storage on headlands, main drains, minor drains and water furrows, was estimated from erosion pin and surface profile measurements. Input from forested upland, input from fields and the output at the outlet of the catchment was estimated with discharge data from gauged streams and flumes. Data for the sediment budget were collected during two ‘wet’-seasons: 1999-2000 and 2000-2001. The results of the sediment budget indicate that this tropical floodplain area is a net source of sediment. Plant cane fields, which do not have a protective trash cover, were the largest net source of sediment during the 1999-2000 season. Sediment input from water furrows was higher, but there was also considerable storage of sediment in this landscape element. Headlands tend to act as sinks. The source or sink function of drains is less clear, but seems to depend on their shape and vegetation cover. An important problem in this study is the high uncertainty in the estimates of the sediment budget components and is, for example, likely to be the cause of the imbalance in the sediment budget. High uncertainties have particularly affected the results from the 20002001 season. The main source of uncertainty is spatial variation in the erosion and deposition processes. Uncertainty has to be taken into consideration when interpreting the budget results. The observation of a floodplain as sediment source contradicts the general understanding that floodplains are areas of sediment storage within river catchments. A second objective of this thesis was therefore to provide an answer to the question: how can floodplains in the tropical North Queensland catchments can be a source of sediment? In geomorphic literature various factors have been pointed out, that could control floodplain erosion processes. However, their importance is not 'uniquely identified'. Among the most apparent factors are the stream power of the floodwater and the resistance of the floodplain surface both through its sedimentary composition and the vegetation cover. If the cultivated floodplains of the North Queensland catchments are considered in the light of these factors, there is a justified reason to expect them to be a sediment source. Cultivation has lowered the resistance of their surface; increased drainage has increased the drainage velocity and flood control structures have altered flooding patterns. For the Ripple Creek floodplain four qualitative scenarios have been developed that describe erosion and deposition under different flow conditions. Two of these scenarios were experienced during the budget study, involving runoff from local hillslopes and heavy rainfall, which caused floodplain erosion. In the longer term larger flood events, involving floodwater from the Herbert River, may lead to different erosion and deposition processes. The present study has shown that the tropical floodplain of the Herbert River catchment can be a source of sediment under particular flow conditions. It has also shown which elements in the sugarcane landscape are the most important sediment sources under these conditions. This understanding will enable sugarcane farmers to further reduce sediment export from cane land and prevent the negative impact this may have on the North Queensland coastal ecosystems.