West Middlands Mosses cSAC, Wybunbury Moss and Abbots Moss

This is the report on Habitats Directive, the Review of Consents Stage 1 and 2 by the Environment Agency of the West Midlands Mosses cSAC, Wybunbury Moss and Abbots Moss. The Habitats Directive has the main aim to promote the maintenance of biodiversity by defining a common framework for the conservation of wild plants and animals and habitats of community interest. The Directive establishes a European ecological network known as "Natura 2000". The network comprises Special Areas of Conservation (SAC) and Special Protection Areas (SPA). In the section on Stage 1 or Screening Process of the Habitat Directive, it is identified the likely impacts upon the West Midlands Mosses cSAC, Wybunbury Moss and Abbots Moss of a project, plan or activities, either alone or in combination with other projects, plans or activities, and considers whether these impacts are likely to be significant. In the section on Stage 2 or Appropiate Assessment of the Habitat Directive, it is considered the impact on the integrity of the West Midlands Mosses cSAC, Wybunbury Moss and Abbots Moss of the projects, plans or activities, either alone or in combination with other projects, plans or activities, with respect to the site’s structure and function and its conservation objectives. Additionally, where these are adverse impacts, an assessment of the potential mitigation of those impacts. The criteria used in this report to identify relevant projects, plans or activities and their impacts are water quality discharge consents, waste management licences, abstraction licences, Integration Pollution Control (IPC) and Integrated Pollution Prevention Control (IPPC) permits. Proformas, hydrogeological and GIS maps are included in the review.

Meres and mosses conservation plan: Rostherne Mere

This is a report on the Conservation Plan for Rostherne Mere. The project primarly involved collating existing information from a variety of sources, supplemented by a limited amount of survey work commissioned for the project, including identification of the surface water catchment, water flows, and land use within the catchment. The section 1 outlines the physical situation of the Site of Special Scientific Interest (SSSI), its geological setting and hydrological regime. A summary of the ecological characteristics, conservation interest and objectives is provided in Section 2, and the issues affecting the site are identified in Section 3. . Operations and mechanisms for addressing the issues are suggested in Section 4, compiled from field visits, information held on file by English Nature and the Environment Agency, and English Nature. The last Section 5 provides a brief summary of the site’s condition and a discussion of the issues and operations suggested. A summary table is provided of the recommended actions for each site. Supporting information on the hydrology and aquatic ecology (where relevant) is provided in appendices.

Reserved parking : marine reserves and small-scale fishing communities: a collection of articles from SAMUDRA report

As the earth’s resources continue to face increasing pressure from a variety of human and natural causes, protection of the environment and biodiversity is a matter of contemporary concern, The conservation of coastal and marine resources, in particular, has become a priority for countries around the world. In this context, marine protected areas (MPAs) are being widely promoted as one of the most effective tools for the conservation of coastal and marine resources. Most MPAs are located in coastal areas of great biodiversity, and hence their development has direct impacts on the lives and livelihoods of coastal communities, especially small-scale and traditional fishing communities. Typically, they are the ones who have to bear the costs of conservation practices–lost livelihood options, expulsion from traditional fishing grounds and living spaces, and violation of human/community rights, to name a few. The articles in this dossier, drawn chronologically from the pages of Samudra Report, the triannual publication of ICSF, draw attention to these issues. They show that conservation and livelihoods are closely intertwined, and that top-down, non-participatory models of conservation can be counter-productive. Despite being poor and powerless, fishing and coastal communities can be powerful allies in conservation efforts, given their longstanding dependence on natural resources and their traditional ecological knowledge systems. As the examples in this dossier reveal, it is possible for fishing communities to protect and conserve the environment, while continuing with sustainable fishing operations. Clearly, only an integrated approach to fisheries management and conservation will prove successful. This dossier will be useful for policymakers, social scientists, non-governmental organizations and others interested in fisheries, conservation, communities and livelihoods.

A pilot survey of deepwater coral/sponge assemblages and their susceptibility to fishing/harvest impacts at the Olympic Coast National Marine Sanctuary (OCNMS). Cruise report for NOAA Ship McARTHUR II Cruise AR-04-04: Leg 2 (June 1-12, 2004)

The offshore shelf and canyon habitats of the OCNMS are areas of high primary productivity and biodiversity that support extensive groundfish fisheries. Recent acoustic surveys conducted in these waters have indicated the presence of hard-bottom substrates believed to harbor unique deep-sea coral and sponge assemblages. Such fauna are often associated with shallow tropical waters, however an increasing number of studies around the world have recorded them in deeper, cold-water habitats in both northern and southern latitudes. These habitats are of tremendous value as sites of recruitment for commercially important fishes. Yet, ironically, studies have shown how the gear used in offshore demersal fishing, as well as other commercial operations on the seafloor, can cause severe physical disturbances to resident benthic fauna. Due to their exposed structure, slow growth and recruitment rates, and long life spans, deep-sea corals and sponges may be especially vulnerable to such disturbances, requiring very long periods to recover. Potential effects of fishing and other commercial operations in such critical habitats, and the need to define appropriate strategies for the protection of these resources, have been identified as a high-priority management issue for the sanctuary.

Lack of mtDNA control region variation in Hainan Eld's deer: Consequence of a recent population bottleneck?

We find no genetic variation at 550bp of mtDNA control region among 55 Hainan Eld's deer in an island population that has suffered recent population contractions. Congeneric species show high levels of variation at this locus. We use a simulation approach to test the likelihood of various bottleneck scenarios, and show, in the context of what is known about the recent demographic history of this population, that there are credible scenarios for a bottleneck driven by hunting pressure in the 1960s that could account for the lack of variation at this locus.

Origin and evolution of the RIG-I like RNA helicase gene family

Background: The DExD/H domain containing RNA helicases such as retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5) are key cytosolic pattern recognition receptors (PRRs) for detecting nucleotide pathogen associated molecular patterns (PAMPs) of invading viruses. The RIG-I and MDA5 proteins differentially recognise conserved PAMPs in double stranded or single stranded viral RNA molecules, leading to activation of the interferon system in vertebrates. They share three core protein domains including a RNA helicase domain near the C terminus (HELICc), one or more caspase activation and recruitment domains (CARDs) and an ATP dependent DExD/H domain. The RIG-I/MDA5 directed interferon response is negatively regulated by laboratory of genetics and physiology 2 (LGP2) and is believed to be controlled by the mitochondria antiviral signalling protein (MAVS), a CARD containing protein associated with mitochondria. Results: The DExD/H containing RNA helicases including RIG-I, MDA5 and LGP2 were analysed in silico in a wide spectrum of invertebrate and vertebrate genomes. The gene synteny of MDA5 and LGP2 is well conserved among vertebrates whilst conservation of the gene synteny of RIG-I is less apparent. Invertebrate homologues had a closer phylogenetic relationship with the vertebrate RIG-Is than the MDA5/LGP2 molecules, suggesting the RIG-I homologues may have emerged earlier in evolution, possibly prior to the appearance of vertebrates. Our data suggest that the RIG-I like helicases possibly originated from three distinct genes coding for the core domains including the HELICc, CARD and ATP dependent DExD/H domains through gene fusion and gene/domain duplication. Furthermore, presence of domains similar to a prokaryotic DNA restriction enzyme III domain (Res III), and a zinc finger domain of transcription factor (TF) IIS have been detected by bioinformatic analysis. Conclusion: The RIG-I/MDA5 viral surveillance system is conserved in vertebrates. The RIG-I like helicase family appears to have evolved from a common ancestor that originated from genes encoding different core functional domains. Diversification of core functional domains might be fundamental to their functional divergence in terms of recognition of different viral PAMPs.

Polymorphic microsatellites in largemouth bronze gudgeon (Coreius guichenoti) developed from repeat-enriched libraries and cross-species amplifications

Largemouth bronze gudgeon (Coreius guichenoti) is a medium-sized fish endemic from the upper Yangtze River of China and its survival is threatened by the construction of the Three Gorges Dam. This study reports 20 new polymorphic microsatellites from a repeat-enriched genomic library with a mean number allele of 5.2, and observed and expected heterozygosities ranging from 0.035 to 1, and from 0.13 to 0.917, respectively. In a cross-species amplification test, nine of the 37 tested loci were found to be also polymorphic in a congeneric species, brass gudgeon (C. heterodon). In addition, other four loci from common carp (Cyprinus carpio) were also polymorphic in C. guichenoti. Out of these 24 polymorphic microsatellites, only three loci significantly deviated from Hardy-Weinberg equilibrium in the sampled population (P < 0.0025), and all pairwise tests for linkage disequilibrium among loci were nonsignificant after applying sequential Bonferroni correction (P > 0.0026). These novel microsatellites provide sufficient levels of polymorphism for studies on population genetics and conservation in C. guichenoti and its related species.

The Yangtze River dolphin or baiji (Lipotes vexillifer): population status and conservation issues in the Yangtze River, China

1. Baiji were sighted 17 times during three recent simultaneous multi-vessel surveys in the Yangtze River, China (November 4-10, 1997; December 4-9, 1998; October 31-November 5, 1999). There were 11 sightings in 1997 (consisting of 17 animals), five in 1998 (seven animals), and two in 1999 (four animals). It was concluded that 13 individuals Could be considered as a minimum number of the baiji currently in the Yangtze River. 2. An annual rate of population decrease was roughly estimated as 10%. From the body sizes observed, the proportions of old, adult and immature individuals were approximately estimated at 57, 26, and 17% respectively. 3. Baiji showed a significant attraction to confluences and sand bars with large eddies. The present distribution range of the baiji is less than 1400 km in length in the Yangtze main river. Distances between the two nearest groups of baiji appear to be increasing. 4. Two typical sightings are described, in which surfacing and movements of baiji were recorded. Baiji were often found swimming together with finless porpoise. In the surveys they occurred in the same group in 63% of occurrences. Interactions between baiji and finless porpoise are described and discussed. 5. Human activities are the main threats to the baiji. Illegal electrical fishing accounted for 40% of known mortalities during the 1990s. Engineering explosions for maintaining navigation channels have become another main cause of baiji deaths. The last hope of saving the species may be to translocate the remaining baiji into a semi-captive reserve. known as the 'Baiji Semi-natural Reserve'. Copyright (C) 2003 John Wiley Sons, Ltd.

The complete mitochondrial genome of the large yellow croaker, Larimichthys crocea (Perciformes, Sciaenidae): Unusual features of its control region and the phylogenetic position of the Sciaenidae

To understand the systematic status of Larimichthys crocea in the Percoidei, we determined the complete mitochondrial (mt) genome sequence using 454 sequencing-by-synthesis technology. The complete mt genome is 16,466 bp in length including the typical structure of 22 tRNAs, 2 rRNAs, 13 protein-coding genes and the noncoding control region (CR). Further sequencing for the complete CR was performed using the primers Cyt b-F and 12S-R on six L crocea individuals and two L polyactis individuals. Interestingly, all seven CR sequences from L crocea were identical while the three sequences from L polyactis were distinct (including one from GenBank). Although the conserved blocks such as TAS and CSB-1, -2, and -3 are readily identifiable in the control regions of the two species, the typical central conserved blocks CSB-D, -E, and -F could not be detected, while they are found in Cynoscion acoupa of Sciaenidae and other Percoidei species. Phylogenetic analysis shows that L crocea is a relatively recently emerged species in Sciaenidae and this family is closely related to family Pomacanthidae within the Percoidei. L crocea, as the first species of Sciaenidae with complete mitochondrial genome available, will provide important information on the molecular evolution of the group. Moreover, the genus-specific pair of primers designed in this study for amplifying the complete mt control region will be very useful in studies on the population genetics and conservation biology of Larimichthys. (c) 2008 Elsevier B.V. All rights reserved.

Isolation and characterization of microsatellite DNA primers in Juniperus przewalskii Kom (Cupressaceae)

Juniperus przewalskii (Cupressaceae) is a dominant tree species endemic to the northeast Qinghai-Tibetan Plateau. This species plays an important role in maintaining the arid ecosystem in this region. However, natural distributions of this species have been declined. In order to develop effective conservation methods, it is important to know the distribution of the genetic diversity within and among populations. In this study, we developed nine new microsatellite loci for this species. We used the combining biotin capture method to enrich AG/CT/AC/GGT microsatellites. The polymorphisms of each locus were further assessed in 12 individuals from four geographically distant populations. The number of alleles per locus varied from three to six and expected heterozygosity ranged from 0.58 to 0.70. These loci together provide a useful tool to investigate the genetic diversity of this species. In addition, all markers have been crossly checked in the other four congeneric species.

Program, abstracts and related documents.

The context: Soil biodiversity and sustainable agriculture; Abstracts - Theme 1: Monitoring and assessment: Bioindicators of soil health: assessment and monitoring for sustainable agriculture; Practical tools to measure soil health and their use by farmers; Biological soil quality from biomass to biodiversity - importance and resilience to management stress and disturbance; Integrated management of plant-parasitic nematodes in maize-bean cropping systems; Microbial quantitative and qualitative changes in soils under different crops and tillage management systems in Brazil; Diversity in the rhizobia associated with Phaseolus vulgaris L: in Ecuador and comparisons with Mexican bean rhizobia; Sistemas integrados ganadería-agricultura en Cuba; Soil macrofauna as bioindicator of soil quality; Biological functioning of cerrado soils; Hydrolysis of fluorescein diacetate as a soil quality indicator in different pasture systems; Soil management and soil macrofauna communities at Embrapa Soybean, Londrina, Brazil; Soil macrofauna in a 24 - year old no-tillage system in Paraná, Brazil; Invertebrate macrofauna of soils inpastures under different forms of management in the cerrado (Brazil); Soil tillage modifies the invertebrate soil macrofauna community; Soil macrofauna in various tillage and land use systems on an oxisols near Londrina, Paraná, Brazil; Interference of agricultural systems on soil macrofauna; Scarab beetle-grub holes in various tillage and crop management systems at Embrapa Soybean, Londrina, Brazil; Biological management of agroecosystems; Soil biota and nutrient dynamics through litterfall in agroforestry system in Rondônia, Amazônia, Brazil; Soil-C stocks and earthworm diversity of native and introduced pastures in Veracruz, Mexico; Theme 2 : Adaptive management: Some thoughts on the effects and implications of the transition from weedy multi-crop to wead-free mono-crop systems in Africa; Towards sustainable agriculture with no-tillage and crop rotation systems in South Brazil; Effect of termites on crusted soil rehabilitation in the Sahel; Management of macrofauna in traditional and conventional agroforestry systems from India with special reference to termites and earthworms; Adaptive management for redeveloping traditional agroecosystems; Conservation and sustainable use of soil biodiversity: learning with master nature!; Convergence of sciences: inclusive technology innovation processes for better integrated crop/vegetation, soil and biodiversity management; Potential for increasing soil biodiversity in agroecosystems; Biological nitrogen fixation and sustainability in the tropics; Theme 3: Research and innovation: Plant flavonoids and cluster roots as modifiers of soil biodiversity; The significance of biological diversity in agricultural soil for disease suppressiveness and nutrient retention; Linking above - and belowground biodiversity: a comparison of agricultural systems; Insect-pests in biologically managed oil and crops: the experience at ICRISAT; Sistemas agricolas micorrizados en Cuba; The effect of velvetbean (Mucuna pruriens) on the tropical earthworm Balanteodrilus pearsei: a management option for maize crops in the Mexican humid tropics; The potential of earthworms and organic matter quality in the rehabilitation of tropical soils; Research and innovation in biological management of soil ecosystems; Application of biodynamic methods in the Egyptian cotton sector; Theme 4: Capacity building and mainstreaming: Soil ecology and biodiversity: a quick scan of its importance for government policy in The Netherlands; Agrotechnological transfer of legume inoculants in Eastern and Southern Africa; Agricultura urbana en Cuba; Soil carbon sequestration for sustaining agricultural production and improving the environment; Conservation and sustainable management of below-ground biodiversity: the TSBF-BGBD network project; The tropical soil biology and fertility institute of CIAT (TSBF); South-South initiative for training and capacity building for the management of soil biology/biodiversity; Strategies to facilititate development and adoption of integrated resource management for sustainable production and productivity improvement; The challenge program on biological nitrogen fixation (CPBNF); Living soil training for farmers: improving knowledge and skills in soil nutrition management; Do we need an inter-governmental panel on land and soil (IPLS)? Protection and sustainable use of biodiversity of soils; Cases Studies -- Plant parasitic nematodes associated with common bean (Phaseolus vulgaris L.) and integrated management approaches; Agrotechnological transfer of legume inoculants in Eastern and Southern Africa; Restoring soil fertility and enhancing productivity in Indian tea plantations with earthworms and organic fertilizers; Managing termites and organic resources to improve soil productivity in the Sahel; Overview and case studies on biological nitrogen fixation: perspectives and limitations; Soil biodiversity and sustainable agriculture: an overview.

RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011.

Building on the planning efforts of the RCN4GSC project, a workshop was convened in San Diego to bring together experts from genomics and metagenomics, biodiversity, ecology, and bioinformatics with the charge to identify potential for positive interactions and progress, especially building on successes at establishing data standards by the GSC and by the biodiversity and ecological communities. Until recently, the contribution of microbial life to the biomass and biodiversity of the biosphere was largely overlooked (because it was resistant to systematic study). Now, emerging genomic and metagenomic tools are making investigation possible. Initial research findings suggest that major advances are in the offing. Although different research communities share some overlapping concepts and traditions, they differ significantly in sampling approaches, vocabularies and workflows. Likewise, their definitions of 'fitness for use' for data differ significantly, as this concept stems from the specific research questions of most importance in the different fields. Nevertheless, there is little doubt that there is much to be gained from greater coordination and integration. As a first step toward interoperability of the information systems used by the different communities, participants agreed to conduct a case study on two of the leading data standards from the two formerly disparate fields: (a) GSC's standard checklists for genomics and metagenomics and (b) TDWG's Darwin Core standard, used primarily in taxonomy and systematic biology.

Plastid microsatellites for the study of genetic variability in the widespread Cephalanthera longifolia, C. damasonium and C. rubra (Neottieae, Orchidaceae), and cross-amplification in other Cephalanthera species

Plastid microsatellite loci developed for Cephalanthera longifolia were used to examine the level of genetic variation within and between populations of the three widespread Cephalanthera species (C. damasonium, C. longifolia and C. rubra). The most detailed sampling was in C. longifolia (42 localities from Ireland to China; 147 individuals). Eight haplotypes were detected. One was detected in the vast majority of individuals and occurred from Ireland to Iran. Three others were only found in Europe (Ireland to Italy, England to Italy and Austria to Croatia). Two were only found in the Middle East and two only in Asia. In C. damasonium, 21 individuals from 10 populations (England to Turkey) were sampled. Only one haplotype was detected. In C. rubra, 34 individuals from eight populations (England to Turkey) were sampled. Although it was not possible to amplify all loci for all samples of this species, nine haplotypes were detected. Short alleles for the trnS-trnG region found in two populations of C. rubra were characterized by sequencing and were caused by deletions of 26 and 30 base pairs. At this level of sampling, it appears that C. rubra shows the greatest genetic variability. Cephalanthera longifolia, C. rubra and C. damasonium have previously been characterized as outbreeding, outbreeding with facultative vegetative reproduction and inbreeding, respectively. Patterns of genetic variation here are discussed in the light of these reproductive system differences. The primers used in these three species of Cephalanthera were also demonstrated to amplify these loci in another five species (C. austiniae, C. calcarata, C. epipactoides, C. falcata and C. yunnanensis). Although it is sometimes treated as a synonym of C. damasonium, the single sample of C. yunnanensis from China had a markedly different haplotype from that found in C. damasonium. All three loci were successfully amplified in two achlorophyllous, myco-heterotrophic species, C. austinae and C. calcarata. © 2010 The Linnean Society of London.

Placing biodiversity in ecosystem models without getting lost in translation

A key challenge to progressing our understanding of biodiversity’s role in the sustenance of ecosystem function is the extrapolation of the results of two decades of dedicated empirical research to regional, global and future landscapes. Ecosystem models provide a platform for this progression, potentially offering a holistic view of ecosystems where, guided by the mechanistic understanding of processes and their connection to the environment and biota, large-scale questions can be investigated. While the benefits of depicting biodiversity in such models are widely recognized, its application is limited by difficulties in the transfer of knowledge from small process oriented ecology into macro-scale modelling. Here, we build on previous work, breaking down key challenges of that knowledge transfer into a tangible framework, highlighting successful strategies that both modelling and ecology communities have developed to better interact with one another. We use a benthic and a pelagic case-study to illustrate how aspects of the links between biodiversity and ecosystem process have been depicted in marine ecosystem models (ERSEM and MIRO), from data, to conceptualisation and model development. We hope that this framework may help future interactions between biodiversity researchers and model developers by highlighting concrete solutions to common problems, and in this way contribute to the advance of the mechanistic understanding of the role of biodiversity in marine (and terrestrial) ecosystems.

Assessing the sensitivity of subtidal sedimentary habitats to pressures associated with marine activities. Phase 1 Report: Rationale and proposed ecological groupings for Level 5 biotopes against which sensitivity assessments would be best undertaken.

The purpose of this study is to produce a series of Conceptual Ecological Models (CEMs) that represent sublittoral rock habitats in the UK. CEMs are diagrammatic representations of the influences and processes that occur within an ecosystem. They can be used to identify critical aspects of an ecosystem that may be studied further, or serve as the basis for the selection of indicators for environmental monitoring purposes. The models produced by this project are control diagrams, representing the unimpacted state of the environment free from anthropogenic pressures. It is intended that the models produced by this project will be used to guide indicator selection for the monitoring of this habitat in UK waters. CEMs may eventually be produced for a range of habitat types defined under the UK Marine Biodiversity Monitoring R&D Programme (UKMBMP), which, along with stressor models, are designed to show the interactions within impacted habitats, would form the basis of a robust method for indicator selection. This project builds on the work to develop CEMs for shallow sublittoral coarse sediment habitats (Alexander et al 2014). The project scope included those habitats defined as ‘sublittoral rock’. This definition includes those habitats that fall into the EUNIS Level 3 classifications A3.1 Atlantic and Mediterranean high energy infralittoral rock, A3.2 Atlantic and Mediterranean moderate energy infralittoral rock, A3.3 Atlantic and Mediterranean low energy infralittoral rock, A4.1 Atlantic and Mediterranean high energy circalittoral rock, A4.2 Atlantic and Mediterranean moderate energy circalittoral rock, and A4.3 Atlantic and Mediterranean low energy circalittoral rock as well as the constituent Level 4 and 5 biotopes that are relevant to UK waters. A species list of characterising fauna to be included within the scope of the models was identified using an iterative process to refine the full list of species found within the relevant Level 5 biotopes. A literature review was conducted using a pragmatic and iterative approach to gather evidence regarding species traits and information that would be used to inform the models and characterise the interactions that occur within the sublittoral rock habitat. All information gathered during the literature review was entered into a data logging pro-forma spreadsheet that accompanies this report. Wherever possible, attempts were made to collect information from UK-specific peer-reviewed studies, although other sources were used where necessary. All data gathered was subject to a detailed confidence assessment. Expert judgement by the project team was utilised to provide information for aspects of the models for which references could not be sourced within the project timeframe. A multivariate analysis approach was adopted to assess ecologically similar groups (based on ecological and life history traits) of fauna from the identified species to form the basis of the models. A model hierarchy was developed based on these ecological groups. One general control model was produced that indicated the high-level drivers, inputs, biological assemblages, ecosystem processes and outputs that occur in sublittoral rock habitats. In addition to this, seven detailed sub-models were produced, which each focussed on a particular ecological group of fauna within the habitat: ‘macroalgae’, ‘temporarily or permanently attached active filter feeders’, ‘temporarily or permanently attached passive filter feeders’, ‘bivalves, brachiopods and other encrusting filter feeders’, ‘tube building fauna’, ‘scavengers and predatory fauna’, and ‘non-predatory mobile fauna’. Each sub-model is accompanied by an associated confidence model that presents confidence in the links between each model component. The models are split into seven levels and take spatial and temporal scale into account through their design, as well as magnitude and direction of influence. The seven levels include regional to global drivers, water column processes, local inputs/processes at the seabed, habitat and biological assemblage, output processes, local ecosystem functions, and regional to global ecosystem functions. The models indicate that whilst the high level drivers that affect each ecological group are largely similar, the output processes performed by the biota and the resulting ecosystem functions vary both in number and importance between groups. Confidence within the models as a whole is generally high, reflecting the level of information gathered during the literature review. Physical drivers which influence the ecosystem were found to be of high importance for the sublittoral rock habitat, with factors such as wave exposure, water depth and water currents noted to be crucial in defining the biological assemblages. Other important factors such as recruitment/propagule supply, and those which affect primary production, such as suspended sediments, light attenuation and water chemistry and temperature, were also noted to be key and act to influence the food sources consumed by the biological assemblages of the habitat, and the biological assemblages themselves. Output processes performed by the biological assemblages are variable between ecological groups depending on the specific flora and fauna present and the role they perform within the ecosystem. Of particular importance are the outputs performed by the macroalgae group, which are diverse in nature and exert influence over other ecological groups in the habitat. Important output processes from the habitat as a whole include primary and secondary production, bioengineering, biodeposition (in mixed sediment habitats) and the supply of propagules; these in turn influence ecosystem functions at the local scale such as nutrient and biogeochemical cycling, supply of food resources, sediment stability (in mixed sediment habitats), habitat provision and population and algae control. The export of biodiversity and organic matter, biodiversity enhancement and biotope stability are the resulting ecosystem functions that occur at the regional to global scale. Features within the models that are most useful for monitoring habitat status and change due to natural variation have been identified, as have those that may be useful for monitoring to identify anthropogenic causes of change within the ecosystem. Biological, physical and chemical features of the ecosystem have been identified as potential indicators to monitor natural variation, whereas biological factors and those physical /chemical factors most likely to affect primary production have predominantly been identified as most likely to indicate change due to anthropogenic pressures.