Appendix A: Rating Scheme for System-Wide Monitoring Questions
Monterey Bay National Marine Sanctuary

The purpose of this appendix is to clarify the 17 questions and possible responses used to report the condition of sanctuary resources in condition reports for all national marine sanctuaries. Individual staff and partners utilized this guidance, as well as their own informed and detailed understanding, of the site to make judgments about the status and trends of sanctuary resources.

The questions derive from the National Marine Sanctuary System’s mission, and a system-wide monitoring framework (NMSP 2004) developed to ensure the timely flow of data and information to those responsible for managing and protecting resources in the ocean and coastal zone, and to those that use, depend on and study the ecosystems encompassed by the sanctuaries⁶². They are used to guide staff and partners at each of the system’s 14 sites in the development of this first periodic sanctuary condition report. Evaluations of status and trends may be based on interpretation of quantitative and, when necessary, non-quantitative assessments and observations of scientists, managers and users.

Ratings for a number of questions depend on judgments involving “ecological integrity,” and an ecosystem’s status with regard to it because one of the foundational principles behind the establishment of marine sanctuaries is to protect ocean ecosystems; however, this concept can be confusing, and interpreted in different ways, so it is important to clarify its application within this report. Ecological integrity implies the presence of naturally occurring species, populations and communities, and ecological processes functioning at appropriate rates, scales and levels of natural variation, as well as the environmental conditions that support these attributes (modified from National Park Service Vital Signs monitoring program). Ecosystems have integrity when they have their native components intact, including abiotic components (the physical elements, such as water and habitats), biodiversity (the composition and abundance of species and communities in an ecosystem) and ecosystem processes (the engines that makes ecosystem work (e.g., space competition, predation, symbioses) (from Parks Canada). For purposes of this report, the level of integrity that is judged to exist is based on the extent to which humans have altered key attributes, and the effect of that change on the ability of an ecosystem to resist continued change and recover from it. The statements for many questions are intended to reflect this judgment. Reference is made in the rating system to “near-pristine” conditions, which, for this report would imply a status as near to an unaltered ecosystem as we can reasonably presume to exist, recognizing that there are virtually no ecosystems on Earth completely free from human influence.

Not all questions, however, use ecological integrity as a basis for judgment. One focuses on the impacts of water quality factors on human health. Another rates the status of key species compared with that expected in an unaltered ecosystem. One rates maritime archaeological resources based on their historical, archaeological, scientific and educational value. Another considers the level and persistence of localized threats posed by degrading archaeological resources. Finally, four specifically ask about the levels of on-going human activity that could affect resource condition.
           
During workshops in which status and trends are rated, experts discuss each question, and relevant data, literature and experience associated with the topic. They then discuss statements that are presented as options for judgments about the status. These statements have been customized for each question. Once a particular statement is agreed upon, a color code and status rating (e.g., good, fair, poor) is assigned. Experts can also decide that the most appropriate rating " N/A" (the question does not apply) or "Undet." (resource status is undetermined).

A subsequent discussion is then held about the trend and whether conditions are improving, remaining the same or declining. Symbols used to indicate trends are the same for all questions: "▲" – conditions appear to be improving; "▬" – conditions do not appear to be changing; "▼" – conditions appear to be declining; and "?" – trend is undetermined.

Question 1 (Water/Stressors): Are specific or multiple stressors, including changing oceanographic and atmospheric conditions, affecting water quality and how are they changing?

This is meant to capture shifts in condition that arise from certain changing physical processes and anthropogenic inputs. Factors resulting in regionally accelerated rates of change in water temperature, salinity, dissolved oxygen or water clarity, could all be judged to reduce water quality. Localized changes in circulation or sedimentation resulting, for example, from coastal construction or dredge spoil disposal, can affect light penetration, salinity regimes, oxygen levels, productivity, waste transport and other factors that influence habitat and living resource quality. Human inputs, generally in the form of contaminants from point or non-point sources, including fertilizers, pesticides, hydrocarbons, heavy metals and sewage, are common causes of environmental degradation, often in combination rather than alone. Certain biotoxins, such as domoic acid, may be of particular interest to specific sanctuaries. When present in the water column, any of these contaminants can affect marine life by direct contact or ingestion, or through bioaccumulation via the food chain.

[Note: Over time, accumulation in sediments can sequester and concentrate contaminants. Their effects may manifest only when the sediments are resuspended during storm or other energetic events. In such cases, reports of status should be made under Question 7 – Habitat Contaminants.]

Question 2 (Water/Eutrophic Condition): What is the eutrophic condition of sanctuary waters and how is it changing?

Nutrient enrichment often leads to planktonic and/or benthic algae blooms. Some affect benthic communities directly through space competition. Overgrowth and other competitive interactions (e.g., accumulation of algal-sediment mats) often lead to shifts in dominance in the benthic assemblage. Disease incidence and frequency can also be affected by algae competition and the resulting chemistry along competitive boundaries. Blooms can also influence water column conditions, including light penetration and plankton availability, which can alter pelagic food webs. Harmful algal blooms often affect resources, as biotoxins are released into the water and air, and deplete oxygen.

Question 3 (Water/Human Health): Do sanctuary waters pose risks to human health and how are they changing?
               
Human health concerns are generally aroused by evidence of contamination (usually bacterial or chemical) in bathing waters or fish intended for consumption. They also emerge when harmful algal blooms are reported or when cases of respiratory distress or other disorders attributable to harmful algal blooms increase dramatically. All of these conditions should be considered for this question.

Some sites may have access to specific information on beach and shellfish conditions. In particular, beaches may be closed when criteria for safe water body contact are exceeded, or shellfish harvesting may be prohibited when contaminant loads or infection rates exceed certain levels. These conditions can be evaluated in the context of the descriptions below.

Question 4 (Water/Human Activities): What are the levels of human activities that may influence water quality and how are they changing?

Among the human activities in or near sanctuaries that affect water quality are those that involve direct discharges (transiting vessels, visiting vessels, onshore and offshore industrial facilities, public wastewater facilities); those that contribute contaminants to stream, river and water control discharges (agriculture, runoff from impermeable surfaces through storm drains, conversion of land use); and those that release airborne chemicals that subsequently deposit via particulates at sea (vessels, land based traffic, power plants, manufacturing facilities, refineries). In addition, dredging and trawling can cause resuspension of contaminants in sediments.

Question 5 (Habitat/Abundance/Distribution): What are the abundance and distribution of major habitat types and how are they changing?

Habitat loss is of paramount concern when it comes to protecting marine and terrestrial ecosystems. Of greatest concern to sanctuaries are changes caused, either directly or indirectly, by human activities. The loss of shoreline is recognized as a problem indirectly caused by human activities. Habitats with submerged aquatic vegetation are often altered by changes in water conditions in estuaries, bays and nearshore waters. Intertidal zones can be affected for long periods by spills or by chronic pollutant exposure. Beaches and haul-out areas can be littered with dangerous marine debris, as well as the water column or benthic habitats. Sandy subtidal areas and hardbottoms are frequently disturbed or destroyed by trawling. Even rocky areas several hundred meters deep are increasingly affected by certain types of trawls, bottom longlines and fish traps. Groundings, anchors and divers damage submerged reefs. Cables and pipelines disturb corridors across numerous habitat types and can be destructive if they become mobile. Shellfish dredging removes, alters and fragments habitats.

The result of these activities is the gradual reduction of the extent and quality of marine habitats. Losses can often be quantified through visual surveys and to some extent using high-resolution mapping. This question asks about the quality of habitats compared to those that would be expected without human impacts. The status depends on comparison to a baseline that existed in the past — one to which restoration efforts might aim.

Question 6 (Habitat/Structure): What is the condition of biologically-structured habitats and how is it changing?

Many organisms depend on the integrity of their habitats, and that integrity is largely determined by the condition of particular living organisms. Coral reefs may be the best known examples of such biologically-structured habitats. Not only is the substrate itself biogenic, but the diverse assemblages residing within and on the reefs depend on and interact with each other in tightly linked food webs. They also depend on each other for the recycling of wastes, hygiene and the maintenance of water quality, among other requirements.

Kelp beds may not be biogenic habitats to the same extent of coral reefs, but kelp provides essential habitat for assemblages that would not reside or function together without it. There are other communities of organisms that are also similarly co-dependent, such as hard bottom communities, which may be structured by bivalves, octocorals, coralline algae or other groups that generate essential habitat for other species. Other examples include intertidal assemblages structured by mussels, barnacles, algae and seagrass beds. This question is intended to address these types of places, where organisms form structures (habitats) on which other organisms depend.

Question 7 (Habitat/Contaminants): What are the contaminant concentrations in sanctuary habitats and how are they changing?

This question addresses the need to understand the risk posed by contaminants within benthic formations, such as soft sediments, hard bottoms or biogenic organisms. In the former two instances, the contaminants can be released by a disturbance. Contaminants can also pass upwards through the food chain when ingested by bottom dwelling prey species. The contaminants of concern generally include pesticides, hydrocarbons and heavy metals, but the specific concerns of individual sanctuaries may differ substantially.

Question 8 (Habitat/Human Activities): What are the levels of human activities that may influence habitat quality and how are they changing?

Human activities that degrade habitat quality affect structural (geological), biological, oceanographic, acoustic or chemical characteristics. Structural impacts include removal or mechanical alteration, including various fishing techniques (trawls, traps, dredges, longlines and even hook-and-line in some habitats), dredging channels and harbors and dumping spoil, vessel groundings, anchoring, laying pipelines and cables, installing offshore structures, discharging drill cuttings, dragging tow cables and placing artificial reefs. Removal or alteration of a habitat’s critical biological components can occur along with several of the above activities, most notably trawling, groundings and cable drags. Marine debris, particularly in large quantities (e.g., lost gillnets and other types of fishing gear), can affect both biological and structural habitat components. Changes in water circulation often occur when channels are dredged, fill is added, coastal areas are reinforced or other construction takes place. These activities affect habitat by changing food delivery, waste removal, water quality (e.g., salinity, clarity and sedimentation), recruitment patterns and a host of other factors. Acoustic impacts can occur to water column habitats and organisms from acute and chronic sources of anthropogenic noise (e.g., shipping, boating, construction). Chemical alterations most commonly occur after spills, with both acute and chronic impacts.

Question 9 (Living Resources/Biodiversity): What is the status of biodiversity and how is it changing?

This is intended to elicit an assessment of the condition of living resources based on expected biodiversity levels and the interactions between species. Intact ecosystems require that all parts not only exist, but that they function together, resulting in natural symbioses, competition and predator-prey relationships. Community integrity, resistance and resilience all depend on these relationships. Abundance, relative abundance, trophic structure, richness, H’ diversity, evenness and other measures are often used to assess these attributes.

Question 10 (Living Resources/Extracted Species): What is the status of environmentally sustainable fishing and how is it changing?

Commercial and recreational harvesting are highly selective activities, for which fishers and collectors target a limited number of species, and often remove high proportions of populations. In addition to removing significant amounts of biomass from the ecosystem, reducing its availability to other consumers, these activities tend to disrupt specific and often critical food web links. When too much extraction occurs (i.e. ecologically unsustainable harvesting), trophic cascades ensue, resulting in changes in the abundance of non-targeted species as well. It also reduces the ability of the targeted species to replenish populations at a rate that supports continued ecosystem integrity.

It is essential to understand whether removals occur at ecologically sustainable levels. Knowing extraction levels and determining the impacts of removal are both ways that help gain this understanding. Measures for target species of abundance, catch amounts or rates (e.g., catch per unit effort), trophic structure and changes in non-target species abundance are all generally used to assess these conditions.

Other issues related to this question include whether fishers are using gear that is compatible with the habitats being fished and whether that gear minimizes by-catch and incidental take of marine mammals. For example, bottom-tending gear often destroys or alters both benthic structure and non-targeted animal and plant communities. "Ghost fishing" occurs when lost traps continue to capture organisms. Lost or active nets, as well as lines used to mark and tend traps and other fishing gear, can entangle marine mammals. Any of these could be considered indications of environmentally unsustainable fishing techniques.

In 2012, the Office of National Marine Sanctuaries led an effort to review and revise the set of questions and their possible responses posed in the condition reports. As part of this effort, some questions were combined, new questions were added and other questions were removed. Question 10, "What is the status of environmentally sustainable fishing and how is it changing?" was removed from the set of questions. This decision was made because of all the questions, it was the only one that focused on a single human activity. The issue of fishing is sufficiently addressed in other questions found in the report, including those related to biodiversity, the status and health of key species, and the status of human activities. For a complete list of the new, revised set of questions, see ONMS 2015. Note that the revised questions are not reflected in the 2015 Monterey Bay National Marine Sanctuary Condition Report Update; however, because of the aforementioned reasons, question 10 was not answered. The new set of questions will be addressed when the condition report is revised in its entirety in the future.

Question 11 (Living Resources/Non-Indigenous Species): What is the status of non-indigenous species and how is it changing?

Non-indigenous species are generally considered problematic, and candidates for rapid response, if found, soon after invasion. For those that become established, their impacts can sometimes be assessed by quantifying changes in the affected native species. This question allows sanctuaries to report on the threat posed by non-indigenous species. In some cases, the presence of a species alone constitutes a significant threat (certain invasive algae). In other cases, impacts have been measured, and may or may not significantly affect ecosystem integrity.

Question 12 (Living Resources/Key Species): What is the status of key species and how is it changing?

Certain species can be defined as "key" within a national marine sanctuary. Some might be keystone species, that is, species on which the persistence of a large number of other species in the ecosystem depends — the pillar of community stability. Their functional contribution to ecosystem function is disproportionate to their numerical abundance or biomass and their impact is therefore important at the community or ecosystem level. Their removal initiates changes in ecosystem structure and sometimes the disappearance of or dramatic increase in the abundance of dependent species. Keystone species may include certain habitat modifiers, predators, herbivores and those involved in critical symbiotic relationships (e.g. cleaning or co-habitating species).

Other key species may include those that are indicators of ecosystem condition or change (e.g., particularly sensitive species), those targeted for special protection efforts or charismatic species that are identified with certain areas or ecosystems. These may or may not meet the definition of keystone, but do require status and trend assessments.

Question 13 (Living Resources/Health of Key Species): What is the condition or health of key species and how is it changing?

For those species considered essential to ecosystem integrity, measures of their condition can be important to determine the likelihood that they will persist and continue to provide vital ecosystem functions. Measures of condition may include growth rates, fecundity, recruitment, age-specific survival, tissue contaminant levels, pathologies (disease incidence tumors, deformities), the presence and abundance of critical symbionts, or parasite loads. Similar measures of condition may also be appropriate for other key species (indicator, protected or charismatic species). In contrast to the question about keystone species question 12 above), the impact of changes in the abundance or condition of key species is more likely to be observed at the population or individual level, and less likely to result in ecosystem or community effects.

Question 14 (Living Resources/Human Activities): What are the levels of human activities that may influence living resource quality and how are they changing?

Human activities that degrade living resource quality cause a loss or reduction of one or more species by disrupting critical life stages, impairing various physiological processes or promoting the introduction of non-indigenous species or pathogens. (Note: Activities that impact habitat and water quality may also affect living resources. These activities are dealt with in questions 4 and 8, and many are repeated here as they also have direct effects on living resources).

Fishing and collecting are the primary means of removing resources. Bottom trawling, seine-fishing and the collection of ornamental species for the aquarium trade are all common examples, some being more selective than others. Chronic mortality can be caused by marine debris derived from commercial or recreational vessel traffic, lost fishing gear and excess visitation, resulting in the gradual loss of some species.

Critical life stages can be affected in various ways. Mortality to adult stages is often caused by trawling and other fishing techniques, cable drags, dumping spoil or drill cuttings, vessel groundings or persistent anchoring. Contamination of areas by acute or chronic spills, discharges by vessels or municipal and industrial facilities can make them unsuitable for recruitment; the same activities can make nursery habitats unsuitable. Although coastal armoring and construction can increase the availability of surfaces suitable for the recruitment and growth of hard bottom species, the activity may disrupt recruitment patterns for other species (e.g., intertidal soft bottom animals) and habitat may be lost.

Spills, discharges and contaminants released from sediments (e.g., by dredging and dumping) can all cause physiological impairment and tissue contamination. Such activities can affect all life stages by reducing fecundity, increasing larval, juvenile and adult mortality, reducing disease resistance and increasing susceptibility to predation. Bioaccumulation allows some contaminants to move upward through the food chain, disproportionately affecting certain species.

Activities that promote introductions include bilge discharges and ballast water exchange, commercial shipping and vessel transportation. Releases of aquarium fish can also lead to species introductions.

Question 15 (Maritime Archaeological Resources/Integrity): What is the integrity of known maritime archaeological resources and how is it changing?

The condition of archaeological resources in a marine sanctuary significantly affects their value for science and education, as well as the resource’s eligibility for listing on the National Register of Historic Places. Assessments of archaeological sites include evaluation of the apparent levels of site integrity, which are based on levels of previous human disturbance and the level of natural deterioration. The historical, scientific and educational values of sites are also evaluated, and are substantially determined and affected by site condition.

Question 16 (Maritime Archaeological Resources/Threat to Environment): Do known maritime archaeological resources pose an environmental hazard and how is this threat changing?

A sinking ship could introduce hazardous materials into the marine environment; this danger is true for historic shipwrecks as well. The issue is complicated by the fact that shipwrecks older than 50 years may be considered historical resources and must, by federal mandate, be protected. Many historic shipwrecks, particularly from the early to mid-twentieth century, can still retain oil and fuel in tanks and bunkers. As shipwrecks age and deteriorate, the potential increases for a release of these materials into the environment.

Question 17 (Maritime Archaeological Resources/Human Activities): What are the levels of human activities that may influence maritime archaeological resource quality and how are they changing?

Some human maritime activities threaten the physical integrity of submerged archaeological resources. Archaeological site integrity is compromised when elements are moved, removed, or otherwise damaged. Threats come from looting by divers, inadvertent damage by scuba diving visitors, improperly conducted archaeology that does not fully document site disturbance, anchoring, groundings, and commercial and recreational fishing activities, among others.

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⁶²In 2012, the Office of National Marine Sanctuaries led an effort to review and revise the set of questions and their possible responses posed in condition reports. The revised questions are not reflected in the 2015 Monterey Bay National Marine Sanctuary Condition Report Update. The revised questions will be addressed when the condition report is revised in its entirety in the future.