ERSEM 15.06: a generic model for marine biogeochemistry and the ecosystem dynamics of the lower trophic levels

The ERSEM model is one of the most established ecosystem models for the lower trophic levels of the marine food-web in the scientific literature. Since its original development in the early nineties it has evolved significantly from a coastal ecosystem model for the North-Sea to a generic tool for ecosystem simulations from shelf seas to the global ocean. The current model release contains all essential elements for the pelagic and benthic part of the marine ecosystem, including the microbial food-web, the carbonate system and calcification. Its distribution is accompanied by a testing framework enabling the analysis of individual parts of the model. Here we provide a detailed mathematical description of all ERSEM components along with case-studies of mesocosm type simulations, water column implementations and a brief example of a full-scale application for the North-West European shelf. Validation against in situ data demonstrates the capability of the model to represent the marine ecosystem in contrasting environments.

iMarNet: an ocean biogeochemistry model intercomparison project within a common physical ocean modelling framework

Ocean biogeochemistry (OBGC) models span a wide variety of complexities, including highly simplified nutrient-restoring schemes, nutrient–phytoplankton–zooplankton–detritus (NPZD) models that crudely represent the marine biota, models that represent a broader trophic structure by grouping organisms as plankton functional types (PFTs) based on their biogeochemical role (dynamic green ocean models) and ecosystem models that group organisms by ecological function and trait. OBGC models are now integral components of Earth system models (ESMs), but they compete for computing resources with higher resolution dynamical setups and with other components such as atmospheric chemistry and terrestrial vegetation schemes. As such, the choice of OBGC in ESMs needs to balance model complexity and realism alongside relative computing cost. Here we present an intercomparison of six OBGC models that were candidates for implementation within the next UK Earth system model (UKESM1). The models cover a large range of biological complexity (from 7 to 57 tracers) but all include representations of at least the nitrogen, carbon, alkalinity and oxygen cycles. Each OBGC model was coupled to the ocean general circulation model Nucleus for European Modelling of the Ocean (NEMO) and results from physically identical hindcast simulations were compared. Model skill was evaluated for biogeochemical metrics of global-scale bulk properties using conventional statistical techniques. The computing cost of each model was also measured in standardised tests run at two resource levels. No model is shown to consistently outperform all other models across all metrics. Nonetheless, the simpler models are broadly closer to observations across a number of fields and thus offer a high-efficiency option for ESMs that prioritise high-resolution climate dynamics. However, simpler models provide limited insight into more complex marine biogeochemical processes and ecosystem pathways, and a parallel approach of low-resolution climate dynamics and high-complexity biogeochemistry is desirable in order to provide additional insights into biogeochemistry–climate interactions.

ERSEM 15.06: a generic model for marine biogeochemistry and the ecosystem dynamics of the lower trophic levels

The European Regional Seas Ecosystem Model (ERSEM) is one of the most established ecosystem models for the lower trophic levels of the marine food web in the scientific literature. Since its original development in the early nineties it has evolved significantly from a coastal ecosystem model for the North Sea to a generic tool for ecosystem simulations from shelf seas to the global ocean. The current model release contains all essential elements for the pelagic and benthic parts of the marine ecosystem, including the microbial food web, the carbonate system, and calcification. Its distribution is accompanied by a testing framework enabling the analysis of individual parts of the model. Here we provide a detailed mathematical description of all ERSEM components along with case studies of mesocosm-type simulations, water column implementations, and a brief example of a full-scale application for the north-western European shelf. Validation against in situ data demonstrates the capability of the model to represent the marine ecosystem in contrasting environments.

High density mangrove plantation enhances surface accretion, surface elevation change, and tree survival in coastal areas susceptible to sea-level rise

Survival, growth, above ground biomass accumulation, soil surface elevation dynamics and nitrogen accumulation in accreted sediments were studied in experimental treatments planted with four different densities (6.96, 3.26, 1.93 and 0.95 seedlings m-2) of the mangrove Rhizophora mucronata in Puttalam Lagoon, Sri Lanka. Measurements were taken over a period of 1171 days and were compared with those from unplanted controls. Trees at the lowest density showed significantly reduced survival, whilst measures of individual tree growth did not differ significantly among treatments. Rates of surface sediment accretion (means ± S.E.) were 13.0 (±1.3), 10.5 (±0.9), 8.4 (±0.3), 6.9 (±0.5) and 5.7 (±0.3) mm yr-1 at planting densities of 6.96, 3.26, 1.93, 0.95, and 0 (unplanted control) seedlings m-2, respectively, showing highly significant differences among treatments. Mean (± S.E.) rates of surface elevation change were much lower than rates of accretion at 2.8 (±0.2), 1.6 (±0.1), 1.1 (±0.2), 0.6 (±0.2) and -0.3 (±0.1) mm yr-1 for 6.96, 3.26, 1.93, 0.95, and 0 seedlings m-2, respectively. All planted treatments appeared to accumulate greater nitrogen concentrations in the sediment compared to the unplanted control, and suggests one potential causal mechanism for the facilitatory effects observed; high densities of plants potentially contribute to the accretion of greater amounts of nutrient rich sediment. While this potential process needs further study, this study demonstrated how higher densities of mangroves enhance rates of sediment accretion and surface elevation, processes that may be crucial in mangrove ecosystem adaptation to sea level rise. There was no evidence that increasing plant density evoked a trade-off with growth and survival of the planted trees. Rather facilitatory effects enhanced survival at high densities, suggesting that local land managers may be able to take advantage of plantation densities to help mitigate sea-level rise effects by encouraging positive soil surface elevation increment, and perhaps even greater nutrient retention to promote mangrove growth and ameliorate nearshore eutrophication in tropical island environments.

Arsenic biogeochemistry as affected by phosphorus fertilizer addition, redox potential and pH in a west Bengal (India) soil

This laboratory experiment systematically examines arsenic, iron, and phosphorus solubilities in soil suspensions as affected by addition of phosphorus fertilizer under different redox potential (Eh) and pH conditions. Under aerobic conditions, As solubility was low, however, under moderately reducing conditions (0, -150 mV), As solubility significantly increased due to dissolution of iron oxy-hydroxides. Upon reduction to -250 mV, As solubility was controlled by the formation of insoluble sulfides, and as a result soluble As contents significantly decreased. Soluble Fe concentration increased from moderate to highly anaerobic conditions; however, it decreased under aerobic conditions likely due to formation of insoluble oxy-hydroxides. A low pH, 5.5, led to increased soluble concentrations of As, Fe, and P. Finally, addition of P-fertilizers resulted in higher soluble P and As, even though the concentration of As did not increased after an addition rate of 600 mg P kg(-1) soil. (c) 2006 Elsevier B.V. All rights reserved.

Genetic structure at range edge: Low diversity and high inbreeding in Southeast Asian mangrove (Avicennia marina) populations

Understanding the genetic composition and mating systems of edge populations provides important insights into the environmental and demographic factors shaping species’ distribution ranges. We analysed samples of the mangrove Avicennia marina from Vietnam, northern Philippines and Australia, with microsatellite markers. We compared genetic diversity and structure in edge (Southeast Asia, and Southern Australia) and core (North and Eastern Australia) populations, and also compared our results with previously published data from core and southern edge populations. Comparisons highlighted significantly reduced gene diversity and higher genetic structure in both margins compared to core populations, which can be attributed to very low effective population size, pollinator scarcity and high environmental pressure at distribution margins. The estimated level of inbreeding was significantly higher in northeastern populations compared to core and southern populations. This suggests that despite the high genetic load usually associated with inbreeding, inbreeding or even selfing may be advantageous in margin habitats due to the possible advantages of reproductive assurance, or local adaptation. The very high level of genetic structure and inbreeding show that populations of A. marina are functioning as independent evolutionary units more than as components of a metapopulation system connected by gene flow. The combinations of those characteristics make these peripheral populations likely to develop local adaptations and therefore to be of particular interest for conservation strategies as well as for adaptation to possible future environmental changes.

Recent changes to the biogeochemistry of Muchalat Inlet, B.C., and the implications for HABs

Senior thesis written for Oceanography 445

Biogeochemistry of Paleozoic brachiopods from New York State and Ontario

A comprehensive elemental, isotopic and microstructural analyses was undertaken of brachiopod calcites from the Hamilton Group (Middle Devonian), Clinton Group (Middle Silurian) and Middle to Upper Ordovician strata of Ontario and New York State. The majority of specimens were microstructurally and chemically preserved in a pristine state, although a number of specimens show some degree of post-depositional alteration. Brachiopod calcites from the Hamilton and Clinton Groups were altered by marine derived waters whereas Trenton Group (Middle Ordovician) brachiopods altered in meteorically derived fluids. Analysis of the elemental and isotopic compositions of pristine Hamilton Group brachiopods indicates there are several chemical relationships inherent to brachiopod calcite. Taxonomic differentiation of Mg, Sr and Na contents was evident in three co-occuring species from the Hamilton Group. Mean Mg contents of pristine brachiopods were respectively Athyris spiriferoides (1309ppm), Mucrospirifer mucronatus (1035ppm) and Mediospirifer audacula (789ppm). Similarly, taxonomic differentiation of shell calcite compositions was observed in co-occuring brachiopods from the Clinton Group (Middle Silurian) and the Trenton Group (Middle Ordovician). The taxonomic control of elemental regulation into shell calcite is probably related to the slightly different physiological systems and secretory mechanisms. A relationship was observed in Hamilton Group species between the depth of respective brachiopod communities and their Mg, Sr and Na contents. These elements were depleted in the shell calcites of deeper brachiopods compared to their counterparts in shallower reaches. Apparently shell calcite elemental composition is related to environmental conditions of the depositional setting, which may have controlled the secretory regime, mineral morphology of shell calcite and precipitation rates of each species. Despite the change in Mg, Sr and Na contents between beds and formations in response to environmental conditions, the taxonomic differentiation of shell calcite composition is maintained. Thus, it may be possible to predict relative depth changes in paleoenvironmental reconstructions using brachiopod calcite. This relationship of brachiopod chemistry to depth was also tested within a transgressiveregressive (T-R) cycle in the Rochester Shale Formation (Middle Silurian). Decreasing Mg, Sr and Na contents were observed in the transition from the shallow carbonates of the Irondequoit Formation to the deeper shales of the lowest 2 m of Rochester Shale. However, no isotopic and elemental trends were observed within the entire T-R cycle which suggests that either the water conditions did not change significantly or that the cycle is illusory. A similar relationship was observed between the Fe and Mn chemistries of shell calcite and redox/paleo-oxygen conditions. Hamilton Group brachiopods analysed from deeper areas of the shelf are enriched in Mn and Fe relative to those from shallow zones. The presence of black shales and dysaerobic faunas, during deposition of the Hamilton Group, suggests that the waters of the northern Appalachian Basin were stratified. The deeper brachiopods were marginally positioned above an oxycline and their shell calcites reflect periodic incursions of oxygen depleted water. Furthermore, analysis of Dalmanella from the black shales of the Collingwood Shale (Upper Ordovician) in comparison to those from the carbonates of the Verulam Formation (Middle Ordovician) confirm the relationship of Fe and Mn contents to periodic but not permanent incursions of low oxygen waters. The isotopic compositions of brachiopod calcite found in Hamilton Group (813C; +2.5% 0 to +5.5% 0; 8180 -2.50/00 to -4.00/00) and Clinton Group (813C; +4.00/00 to +6.0; 8180; -1.8% 0 to -3.60/ 00) are heavier than previously reported. Uncorrected paleotemperatures (assuming normal salinity, 0% 0 SMOW and no fractionation effects) derived from these isotopic values suggest that the Clinton sea temperature (Middle Silurian) ranged from 18°C to 28°C and Hamilton seas (Middle Devonian) ranged between 24°C and 29°C. In addition, the isotopic variation of brachiopod shell calcite is significant and is related to environmental conditions. Within a single time-correlative shell bed (the Demissa Bed; Hamilton Group) a positive isotopic shift of 2-2.5% 0 in 013C compositions and a positive shift of 1.0-1.50/00 in 0180 composition of shell calcite is observed, corresponding with a deepening of brachiopod habitats toward the axis of the Appalachian Basin. Moroever, a faunal succession from deeper Ambocoelia dominated brachiopod association to a shallow Tropidoleptus dominated assocation is reflected by isotopic shifts of 1.0-1.50/00. Although, other studies have emphasized the significance of ±20/oo shifts in brachiopod isotopic compositions, the recognition of isotopic variability in brachiopod calcite within single beds and within depositional settings such as the Appalachian Basin has important implications for the interpretation of secular isotopic trends. A significant proportion of the variation observed isotopic distribution during the Paleozoic is related to environmental conditions within the depositional setting.

Production and Characterization of Lignin Peroxidases from Mangrove Ascomycetes

In this thesis, the production and characterization of ligninolytic enzymes using the fungi isolated from mangrove area are studied. The objective of the present work are isolation and screening of dye decolorizing micro-organisms from mangrove area, screening of the selected microorganisms for the production of lignin degrading enzymes, identification of the potent micro-organisms, characterization of the crude enzyme, lignin peroxidase, of the selected fungi—Aspergillus sp. SIP 11 and Penicillium sp. SIP 10 etc. This included the determination of the optimum pH, temperature, veratryl alcohol and H2O2 concentration. Besides the stability of crude LiP at different pHs and temperatures were studied. The immense applications, particularly in bioremediation, to which the lignin degrading micro-organisms could be used make this study important, the ascomycetes and deuteromycetes fungi, especially form the marine environment were studied with respect to their ligninolytic enzyme system making this study an initial step in unraveling the vast hidden potential of these microbes in bioremediation, the marine microbes are halophilic in nature which make them better suited to cope with the high salinity of industrial effluents thereby giving them added advantage in the filed of bioremediation. The thesis deals with the isolation and screening of lignin degrading enzyme-producing microbes from mangrove area. The identification of the most potent fungal isolates and characterization of LiP from these are also done.

Modelling of Geochemical Processes in Mangrove Ecosystem

The mangrove ecosystem is one of the earth’s most endangered ecosystems. In this study, geochemical features of three mangrove ecosystems, Mangalavanam, Vypeen and Nettoor were compared. Water, sediment and core samples were collected from these stations for a period of one year. Nutrients, organic compounds orgnic carbon and hydrographical parameters of the samples were estimated. The present study revealed higher concentration of carbon in the surface sediments. The major temporary or ultimate sink for various pollutants in estuaries is the sedimentary reservoir, including intertidal areas. In the present study, higher values for dissolved nutrients, POC and carbohydrates were observed during low tide.

Intervariability of Phosphorus Speciation in Selected Mangrove Ecosystems Around the Greater Cochin

Mangrove forests are best developed on tropical shorelines where there is an extensive intertidal zone, with an abundant supply of fine-grained sediment. It receives a mixture of liable and refractory organic and inorganic phosphorus compounds from the overlying water and the surrounding landmasses. Organic phosphorus is not available for mangrove plant nutrition. While inorganic phosphate represents the largest potential pool of plant-available and which are bound in the form of Ca, Fe and Al phosphate. It deals with the scientific investigations on mangrove systems in the Kerala coastline and to investigate nutrient distribution of mangrove ecosystems of greater Cochin area. It discusses the description of study areas such as Murikkumpadam-Vypeen Island and Aroor. Then it deals with the spatial and seasonal distribution of dissolved ammonia, nitrite, nitrate, inorganic phosphate, organic phosphate and the total phosphorus in surface waters of mangrove fringed creeks. Then it discusses the geochemical compositions of mangrove-fringed sediments and also the chemical speciation of phosphorus in sediment cores.

Biogeochemistry of trace metals in the Indian EEZ of the Arabian Sea and Bay of Bengal

The present study has been initiated to unravel the distribution of trace metals and its geochemical behavior in the Indian EEZ of the Arabian Sea and Bay of Bengal. Trace metal accumulation in aquatic consumers is of interest to ecologists and environmentalists so as to understand the fate and effect of contaminants in the food web dynamics and the biogeochemical cycling of trace metals. It is well established that oceanic distribution of macronutrients such as nitrate, phosphate and silicate provide critical to biological growth and related geochemical processes. In this study it can be inferred, that there is a need for a better understanding of background informations on trace metal concentrations with respect to space and time and their fluctuations in the Arabian Sea and Bay of Bengal zooplankton. Without a sound knowledge on spatio-temporal fluctuations, it will be impossible to differentiate anthropogenic metal inputs from natural background concentrations with a routine biomonitoring programme. Fe, Cu, Zn, Cd & Pb showed a slight enrichment in zooplankton from the Arabian Sea during spring intermonsoon compared to intermonsoon fall. The relative enrichment of Fe, Cu & Zn in zooplankton from the Arabian Sea during intermonsoon spring than intermonsoon fall was due to favourable bioaccumulation factors of these elements during this season. Nevertheless this study can be looked upon as a starting point for further investigations on these biogeochemically important processes, which are vital in addressing the dynamics of productivity of waters.

Studies on the Benthic Fauna of the Mangrove Swamps of Cochin Area

Division of Marine Biology, Micrbiology and Biochemistry,Cochin University of Science and Technology