A general framework for aquatic biogeochemical models

One of the most of challenging steps in the development of coupled hydrodynamic-biogeochemical models is the combination of multiple, often incompatible computer codes that describe individual physical, chemical, biological and geological processes. This “coupling” is time-consuming, error-prone, and demanding in terms of scientific and programming expertise. The open source, Fortran-based Framework for Aquatic Biogeochemical Models addresses these problems by providing a consistent set of programming interfaces through which hydrodynamic and biogeochemical models communicate. Models are coded once to connect to FABM, after which arbitrary combinations of hydrodynamic and biogeochemical models can be made. Thus, a biogeochemical model code works unmodified within models of a chemostat, a vertically structured water column, and a three-dimensional basin. Moreover, complex biogeochemistry can be distributed over many compact, self-contained modules, coupled at run-time. By enabling distributed development and user-controlled coupling of biogeochemical models, FABM enables optimal use of the expertise of scientists, programmers and end-users.

Polychaete burrows harbour distinct microbial communities in oil-contaminated coastal sediments

Previous studies have shown that the bioturbating polychaete Hediste (Nereis) diversicolor can affect the composition of bacterial communities in oil-contaminated sediments, but have not considered diversity specifically within bioturbator burrows or the impact on microbial eukaryotes. We tested the hypothesis that H. diversicolor burrows harbour different eukaryotic and bacterial communities compared with un-bioturbated sediment, and that bioturbation stimulates oil degradation. Oil-contaminated sediment was incubated with or without H. diversicolor for 30 days, after which sediment un-affected by H. diversicolor and burrow DNA/RNA samples were analysed using quantitative reverse transcription PCR (Q-RT-PCR) and high-throughput sequencing. Fungi dominated both burrow and un-bioturbated sediment sequence libraries; however, there was significant enrichment of bacterivorous protists and nematodes in the burrows. There were also significant differences between the bacterial communities in burrows compared with un-bioturbated sediment. Increased activity and relative abundance of aerobic hydrocarbon-degrading bacteria in the burrows coincided with the significant reduction in hydrocarbon concentration in the bioturbated sediment. This study represents the first detailed assessment of the effect of bioturbation on total microbial communities in oil-contaminated sediments. In addition, it further shows that bioturbation is a significant factor in determining microbial diversity within polluted sediments and plays an important role in stimulating bioremediation.

Biological Communities at Marine Shallow-Water Vent and Seep Sites

The review compiles, for the first time, data on the communities at 62 shallow-water hydrothermal vent and cold seep sites. ‘Shallow sites’ are defined as sites no deeper than 200 m. The communities at these sites are also compared with communities in reducing sediments at similar depths. Below 200 m, vent and seep obligate species tend to dominate the fauna living in areas where reducing fluids are released from the seabed. At the shallow sites, vent and seep obligate species of fauna are rare, only eight having being reported from shallow vents. No definite seep obligates have been found. Shallow vents and seeps are colonized by communities that consist of a subset of the background fauna, especially those species that are less sensitive to hydrogen sulphide toxicity. Conversely the zones directly surrounding shallow vent and seeps sites with varied topography, substrate type and food supply, often have a higher species diversity than the background area. The reasons for these differences are discussed.

Probabilistic Models to Describe the Dynamics of Migrating Microbial Communities

In all but the most sterile environments bacteria will reside in fluid being transported through conduits and some of these will attach and grow as biofilms on the conduit walls. The concentration and diversity of bacteria in the fluid at the point of delivery will be a mix of those when it entered the conduit and those that have become entrained into the flow due to seeding from biofilms. Examples include fluids through conduits such as drinking water pipe networks, endotracheal tubes, catheters and ventilation systems. Here we present two probabilistic models to describe changes in the composition of bulk fluid microbial communities as they are transported through a conduit whilst exposed to biofilm communities. The first (discrete) model simulates absolute numbers of individual cells, whereas the other (continuous) model simulates the relative abundance of taxa in the bulk fluid. The discrete model is founded on a birth-death process whereby the community changes one individual at a time and the numbers of cells in the system can vary. The continuous model is a stochastic differential equation derived from the discrete model and can also accommodate changes in the carrying capacity of the bulk fluid. These models provide a novel Lagrangian framework to investigate and predict the dynamics of migrating microbial communities. In this paper we compare the two models, discuss their merits, possible applications and present simulation results in the context of drinking water distribution systems. Our results provide novel insight into the effects of stochastic dynamics on the composition of non-stationary microbial communities that are exposed to biofilms and provides a new avenue for modelling microbial dynamics in systems where fluids are being transported.

Historical data reveal power-law dispersal patterns of invasive aquatic species.

Understanding how invasive species spread is of particular concern in the current era of globalisation and rapid environmental change. The occurrence of super-diffusive movements within the context of Lévy flights has been discussed with respect to particle physics, human movements, microzooplankton, disease spread in global epidemiology and animal foraging behaviour. Super-diffusive movements provide a theoretical explanation for the rapid spread of organisms and disease, but their applicability to empirical data on the historic spread of organisms has rarely been tested. This study focuses on the role of long-distance dispersal in the invasion dynamics of aquatic invasive species across three contrasting areas and spatial scales: open ocean (north-east Atlantic), enclosed sea (Mediterranean) and an island environment (Ireland). Study species included five freshwater plant species, Azolla filiculoides, Elodea canadensis, Lagarosiphon major, Elodea nuttallii and Lemna minuta; and ten species of marine algae, Asparagopsis armata, Antithamnionella elegans, Antithamnionella ternifolia, Codium fragile, Colpomenia peregrina, Caulerpa taxifolia, Dasysiphonia sp., Sargassum muticum, Undaria pinnatifida and Womersleyella setacea. A simulation model is constructed to show the validity of using historical data to reconstruct dispersal kernels. Lévy movement patterns similar to those previously observed in humans and wild animals are evident in the re-constructed dispersal pattern of invasive aquatic species. Such patterns may be widespread among invasive species and could be exacerbated by further development of trade networks, human travel and environmental change. These findings have implications for our ability to predict and manage future invasions, and improve our understanding of the potential for spread of organisms including infectious diseases, plant pests and genetically modified organisms.

Photoacclimation of natural phytoplankton communities

Phytoplankton regulate internal pigment concentrations in response to light and nutrient availability. Chlorophyll to carbon ratios (Chl:Cphyto) are commonly reported as a function of growth irradiance (Eg) for evaluating the photoacclimation response of phytoplankton. In contrast to most culture experiments, natural phytoplankton communities experience fluctuating environmental conditions making it difficult to compare field and lab observations. Observing and understanding photoacclimation in nature is important for deciphering changes in Chl:Cphyto resulting from environmental forcings and for accurately estimating net primary production (NPP) in models which rely on a parameterized description of photoacclimation. Here we employ direct analytical measurements of Cphyto and parallel high-resolution biomass estimates from particulate backscattering (bbp) and flow cytometry to investigate Chl:Cphyto in natural phytoplankton communities. Chl:Cphyto observed over a wide range of Eg in the field was consistent with photoacclimation responses inferred from satellite observations. Field-based photoacclimation observations for a mixed natural community contrast with laboratory results for single species grown in continuous light and nutrient replete conditions. Applying a carbon-based net primary production (NPP) model to our field data for a north-south transect in the Atlantic Ocean results in estimates that closely match 14C depth-integrated NPP for the same cruise and with historical records for the distinct biogeographic regions of the Atlantic Ocean. Our results are consistent with previous satellite and model observations of cells growing in natural or fluctuating light and showcase how direct measurements of Cphyto can be applied to explore phytoplankton photophysiology, growth rates, and production at high spatial resolution in-situ.

Dip in the gene pool: metagenomic survey of natural coccolithovirus communities

Despite the global oceanic distribution and recognised biogeochemical impact of coccolithoviruses (EhV), their diversity remains poorly understood. Here we employed a metagenomic approach to study the occurrence and progression of natural EhV community genomic variability. Analysis of EhV metagenomes from the early and late stages of an induced bloom led to three main discoveries. First, we observed resilient and specific genomic signatures in the EhV community associated with the Norwegian coast, which reinforce the existence of limitations to the capacity of dispersal and genomic exchange among EhV populations. Second, we identified a hyper-variable region (approximately 21kbp long) in the coccolithovirus genome. Third, we observed a clear trend for EhV relative amino-acid diversity to reduce from early to late stages of the bloom. This study validated two new methodological combinations, and proved very useful in the discovery of new genomic features associated with coccolithovirus natural communities.

Bacterioviridins: novel sedimentary chlorins providing evidence for oxidative processes affecting palaeobacterial communities

Of novel sedimentary transformation products of bacteriochlorophyll a, 7,8-didehydro derivatives (Bacterioviridins), has been identified using high performance liquid chromatography with photodiode array detection and atmospheric pressure chemical ionisation liquid chromatography-multistage mass spectrometry. The derivatives occur in a range of sediments including Priest Pot (UK), les Salines de la Trinital, Ebre delta (Spain), Sutton-on-the-Forest (UK) and Certes (France). The Bacterioviridins are products of oxidative transformation of bacteriochlorophyll a, and their presence in sediments indicates exposure of the bacterial community to oxygen.

Modelling the future biogeography of North Atlantic zooplankton communities in response to climate change

Advances in habitat and climate modelling allow us to reduce uncertainties of climate change impacts on species distribution. We evaluated the impacts of future climate change on community structure, diversity, distribution and phenology of 14 copepod species in the North Atlantic. We developed and validated habitat models for key zooplankton species using continuous plankton recorder (CPR) survey data collected at mid latitudes of the North Atlantic. Generalized additive models (GAMs) were applied to relate the occurrence of species to environmental variables. Models were projected to future (2080–2099) environmental conditions using coupled hydroclimatix–biogeochemical models under the Intergovernmental Panel on Climate Change (IPCC) A1B climate scenario, and compared to present (2001–2020) conditions. Our projections indicated that the copepod community is expected to respond substantially to climate change: a mean poleward latitudinal shift of 8.7 km per decade for the overall community with an important species range variation (–15 to 18 km per decade); the species seasonal peak is expected to occur 12–13 d earlier for Calanus finmarchicus and C. hyperboreus; and important changes in community structure are also expected (high species turnover of 43–79% south of the Oceanic Polar Front). The impacts of the change expected by the end of the century under IPCC global warming scenarios on copepods highlight poleward shifts, earlier seasonal peak and changes in biodiversity spatial patterns that might lead to alterations of the future North Atlantic pelagic ecosystem. Our model and projections are supported by a temporal validation undertaken using the North Atlantic climate regime shift that occurred in the 1980s: the habitat model built in the cold period (1970–1986) has been validated in the warm period (1987–2004).

4. Nomenclature and syntaxonomy of castellano-cantabrian Thymus mastigophorus communities

Rivas Goday, Borja & Izco (Anales Inst. Bot. Cavanilles 26: 153 et seq. including table 2; 1970) described a Thymus mastigophorus association found on the «páramos» of Masa and La Brújula in the province of Burgos, Spain.

List of species and vegetal communities of Isla Grosa (Murcia, España)

The vegetal population of Isla Grosa, island located in the neighbourhood of Mar Menos (Mediterranean Sea), is studies. It is registered the presence of the association Mayteno-Periplocetum. Likewise a registrer of other species is given, being this the first vegetal contribution to this volcanic island.

Validations of high-rank syntaxa in Potamogetonetea and Scheuchzerio-Caricetea fuscae

This paper presents the validation of five syntaxonomic concepts –two orders (Callitricho hamulatae-Ranunculetalia aquatilis, Zannichellietalia pedicellatae) and three alliances (Ranunculion aquatilis, Nelumbion nuciferae and Caricion viridulo-trinervis).

Playback Theatre: the art of being oneself. A tool for empowerment and real change for individuals and communities

This article presents the application of a theatrical technique—Playback Theatre, which was developed in the United States during the 1970s—to social intervention, as a narrative and listening space that confers value and dignity upon the person and the unique and distinct individual experiences that facilitate their social and relational integration. This art of being oneself, as the author states, uses the oral tradition and spontaneous and creative communication of psychodrama and combines them with theatrical expression. This technique has been shown to be pertinent to both community social work and support groups for persons in problematic situations. The aim of this is to celebrate some specific moment of their lives, as individuals or as a community, and to define strategies for improving living conditions or resolving or alleviating conflicts. It is also used to assess the achievements of the proposed objectives, to strengthen the motivation to change and to transform existing relationships into collaborative ones. This is possible not only owing to the participation of persons, but also to the assumption of different roles that can permit the overcoming of certain traumatic events.In addition to support groups, it is used for the training and supervision of social work professionals. The theatrical technique in question allows them to assume roles as diverse as narrator, audience or actor, whether simultaneously or successively. Taking the role of «performer» or guide to the theatrical action requires prior preparation in order for the group of participants to be able to pool their individualities and their emotions and reflect on them. The participatory methodology that Playback Theatre proposes is important in community social work and is posed in a new and transformative key.