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Neira, C, Cossaboon J, Mendoza G, Hoh E, Levin LA.  2017.  Occurrence and distribution of polycyclic aromatic hydrocarbons in surface sediments of San Diego Bay marinas. Marine Pollution Bulletin. 114:466-479.   10.1016/j.marpolbul.2016.10.009   Abstract

Polycyclic aromatic hydrocarbons (PAHs) have garnered much attention due to their bioaccumulation, carcinogenic properties, and persistence in the environment. Investigation of the spatial distribution, composition, and sources of PAHs in sediments of three recreational marinas in San Diego Bay, California revealed significant differences among marinas, with concentrations in one site exceeding 16,000 ng g− 1. ‘Hotspots’ of PAH concentration suggest an association with stormwater outfalls draining into the basins. High-molecular weight PAHs (4–6 rings) were dominant (> 86%); the average percentage of potentially carcinogenic PAHs was high in all sites (61.4–70%) but ecotoxicological risks varied among marinas. Highly toxic benzo(a)pyrene (BaP) was the main contributor (> 90%) to the total toxic equivalent quantity (TEQ) in marinas. PAHs in San Diego Bay marina sediments appear to be derived largely from pyrogenic sources, potentially from combustion products that reach the basins by aerial deposition and stormwater drainage from nearby streets and parking lots.

Zirino, A, Elwany H, Facca C, Maicu F, Neira C, Mendoza G.  2016.  Nitrogen to phosphorus ratio in the Venice (Italy) Lagoon (2001-2010) and its relation to macroalgae. Marine Chemistry. 180:33-41.   10.1016/j.marchem.2016.01.002   AbstractWebsite

Analysis of the annually-averaged 2001-2010 monthly nutrient data from 13 stations in the Venice Lagoon (Italy) shows that the concentrations of dissolved nitrogen (N) species, measured as total dissolved N (TDN), have increased over time while that of phosphorus (P) species, measured as total dissolved P (TDP) have decreased. During the study period, the TDN/TDP ratio in the lagoon rose from about 46:1 to 100:1 (by atoms), a level at which the growth of benthic macroalgae is favored over that of sea grasses. The increase of the TDN/TDP ratio appears to be caused by two factors: (1) a small, but increasing amount of N in river water entering the lagoon, and (2) low P input combined with adsorption and entrapment of orthophosphate on colloidal iron oxides and carbonates at the water-sediment interface. This second mechanism would explain the increase in the TDN/TDP ratio, principally in zones of low salinity, where hydrodynamic residence times are long enough to permit N enrichment and result in macroalgal growth preferentially in the central, landward, side of the lagoon. However, an examination of the algal coverage of the lagoon floor from 2002 to 2010, indicates that while macroalgal abundance may be influenced by the N/P ratio, the spatial and temporal distribution during this period cannot be explained solely by this one feature. Nonetheless, this work points to the importance of considering the contributions that sediments in shallow lagoons make to the over-all system productivity and ecology and may be applicable to other shallow environments. (C) 2016 Elsevier B.V. All rights reserved.

Neira, C, Mendoza G, Porrachia M, Stransky C, Levin LA.  2015.  Macrofaunal recolonization of copper-contaminated sediments in San Diego Bay. Marine Pollution Bulletin. 101:794-804.   10.1016/j.marpolbul.2015.09.023   AbstractWebsite

Effects of Cu-loading on macrofaunal recolonization were examined in Shelter Island Yacht Basin (San Diego Bay, California). Sediments with high and low Cu levels were defaunated and Cu-spiked, translocated, and then placed back into the environment These demonstrated that the alteration observed in benthic communities associated with Cu contamination occurs during initial recolonization. After a 3-month exposure to sediments with varying Cu levels, two primary colonizing communities were identified: (1) a "mouth assemblage" resembling adjacent background fauna associated with low-Cu levels that was more diverse and predominantly dominated by surface- and subsurface-deposit feeders, burrowers, and tube builders, and (2) a "head assemblage" resembling adjacent background fauna associated with high-Cu concentrations, with few dominant species and an increasing importance of carnivores and mobile epifauna. Cu loading can cause reduced biodiversity and lower structural complexity that may last several months if high concentrations persist, with a direct effect on community functioning. (C) 2015 Elsevier Ltd. All rights reserved.

Neira, C, Levin LA, Mendoza G, Zirino A.  2014.  Alteration of benthic communities associated with copper contamination linked to boat moorings. Marine Ecology-an Evolutionary Perspective. 35:46-66.   10.1111/maec.12054   AbstractWebsite

Although copper (Cu) is an essential element for life, leaching from boat paint can cause excess environmental loading in enclosed marinas. The effects of copper contamination on benthic macrofaunal communities were examined in three San Diego Bay marinas (America's Cup, Harbor Island West and East) in Southern California, USA. The distribution of Cu concentration in sediments exhibited a clear spatial gradient, with hotspots created by the presence of boats, which in two marinas exceeded the effect range medium (ERM). Elevated sediment Cu was associated with differences in benthic assemblages, reduced species richness and enhanced dominance in America's Cup and Harbor Island West, whereas Harbor Island East did not appear to be affected. At sites without boats there were greater abundances of some amphipods such as the species Desdimelita sp., Harpinia sp., Aoroides sp., Corophium sp., Podocerus sp., bivalves such as Lyonsia californica, Musculista senhousia, Macoma sp., and polychaetes such as Diplocirrus sp. In contrast, at sites with boats, densities of Pseudopolydora paucibranchiata, Polydora nuchalis, Euchone limnicola, Exogone lourei, Tubificoides spp. were enhanced. The limited impact on Harbor Island East suggests not only lower Cu input rates and increased water flushing and mixing, but also the presence of adequate defense mechanisms that regulate availability and mitigate toxic impacts. At all three marinas, Cu in tissues of several macrobenthic species exhibited Cu bioaccumulation above levels found in the surrounding environment. The annelids Lumbrineris sp. and Tubificoides spp., and the amphipod Desdimelita sp. contained high levels of Cu, suggesting they function as Cu bioaccumulators. The spionid polychaetes Polydora nuchalis and Pseudopolydora paucibranchiata had much lower Cu concentrations than surrounding sediments, suggesting they function as Cu bioregulators. The macrobenthic invertebrates in San Diego Bay marinas that tolerate Cu pollution (e.g. P.nuchalis, P.paucibranchiata, Euchone limnicola, Typosyllis sp., Tubificoides sp.) may function as indicators of high-Cu conditions, whereas the presence of Cu-sensitive species (e.g. Podocerus sp., Aoroides sp., Harpinia sp., Macoma sp., Lyonsia californica) may indicate healthier conditions (less Cu-stressed). Parallel responses by faunas of Shelter Island Yacht Basin, also in San Diego Bay, suggest potential for development of regional Cu contamination assessment criteria, and call for functional comparisons with other marinas and coastal water bodies.

Zirino, A, Elwany H, Neira C, Maicu F, Mendoza G, Levin LA.  2014.  Salinity and its variability in the Lagoon of Venice, 2000–2009. Advances in Oceanography and Limnology. 5:41-59.: Taylor & Francis   10.1080/19475721.2014.900113   Abstract

Yearly averages computed from monthly and bimonthly salinity data collected between 2000 and 2009 from 13 broadly spaced stations in the Venice Lagoon were analysed in view of 30 min data collected semi-continuously during 2009 at nine similarly located stations. Data from all stations and all years indicate that, based on yearly averages, the lagoon may be divided along its major (long) axis into three areas: 1) a northern, freshwater impacted area (S = <28 PSU) of high, tidally-caused, variability, 2) a southern, marine, zone of S >32 PSU of low, tidally-caused, variability, and 3) an intermediate zone. Salinity changes are closely associated with rainfall events, and the incoming freshwater is consistently distributed throughout the lagoon by tidal action. Much variability is simply a result of the forward and backward motion of the tides and is not caused by a salinity change in the water itself. The consistency of the 2000?2009 data and the historical (to 1961) watershed record support the hypothesis that the Venice Lagoon has been and is currently at steady-state with respect to its salinity distribution. As such, it is conducive to the development of (at least) three separate ecosystems.

Neira, C, King I, Mendoza G, Sellanes J, De Ley P, Levin LA.  2013.  Nematode community structure along a central Chile margin transect influenced by the oxygen minimum zone. Deep Sea Research Part I: Oceanographic Research Papers. 78:1-15.   10.1016/j.dsr.2013.04.002   AbstractWebsite

Nematodes are among the metazoans most tolerant of low-oxygen conditions and play major roles in seafloor ecosystem processes. Nematode communities were studied in sediments off Concepción, Central Chile, spanning the outer shelf within the OMZ (122 m) to the mid-lower continental slope (972 m) beneath the OMZ. The total density and biomass of nematodes (core depth 0–10 cm) ranged from 677 to 2006 ind. 10 cm−2, and 168.4 to 506.5 µg DW 10 cm−2, respectively. Among metazoan meiofaunal taxa, nematodes predominated at all sites both in terms of relative abundance (83.7–99.4%) and biomass (53.8–88.1%), followed by copepods, nauplii and polychaetes. Nematodes were represented by 33 genera distributed among 17 families, with densities greatest at low oxygen sites (122–364 m; ~2000 ind. 10 cm−2). Nematode generic and trophic diversity, and individual biomass were lowest, and Rank 1 dominance was highest, at the most oxygen-depleted site (122 m), despite the fact that the organic carbon content of the sediment was maximal at this depth. At the most oxygenated slope sites (827 and 972 m), all of Wieser's nematode feeding groups were represented. In contrast, at the lowest-oxygen site, only selective deposit (bacterial) feeders (1A) were present, indicating a reduction in trophic complexity. A large percentage of nematodes inhabited subsurface sediment layers (>1 cm). At deeper, more oxygenated sites (827 and 972 m), nematode individual biomass increased downcore, while within the OMZ, nematode biomass was low and remained relatively uniform through the sediment column. The concentration of nematodes in deeper sediment layers, the vertical distribution of the feeding groups, as well as the high nutritional quality of the deeper layers, suggest a differential resource partitioning of the food available, which may reduce interspecific competition.

Zirino, A, Neira C, Maicu F, Levin LA.  2013.  Comments on and implications of a steady-state in coastal marine ecosystems. Chemistry & Ecology. 29:86-99.   10.1080/02757540.2012.696613   AbstractWebsite

Coastal ecosystems can be thought of as being established by a number of physico-geochemical drivers, e.g. geochemistry and bathymetry of the basins, climate, tidal and freshwater flows, natural and anthropogenic inputs of nutrients and toxins, all of which exert an influence on the resulting communities of organisms. Depending on the interactions among the major drivers, ecosystems may occur on both large and small scales and be basin-wide or within basins. For individual and separate ecosystems to exist with some permanence in time, e.g. reach a steady-state, they also have to be ‘defended’. Defences are mechanisms that counter changes to maintain the status quo. We argue, and present evidence to support the notion, that the defence mechanisms are inextricably tied to primary production and the biogeochemical cycling of organic matter and provide buffers that mitigate potentially adverse impacts by trace toxins. Colloid pumping, production of complexing ligands and sulfide formation are some of the mechanisms that control trace substances. Current methods for assessing ecosystems do not address the issue of steady-state, nor do they take account of defence activities, e.g. buffering. Therefore, they cannot assess the ‘robustness’ of ecosystems or their ability to resist change, for good or bad. Also, defence mechanisms may, for a time, mask future potentially serious impacts, suggesting that monitoring efforts with limited budgets should consider the measurement of the inputs into ecosystems as well as the immediate or short-term result of the inputs. [ABSTRACT FROM PUBLISHER]Copyright of Chemistry & Ecology is the property of Taylor & Francis Ltd and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Neira, C, Mendoza G, Levin LA, Zirino A, Delgadillo-Hinojosa F, Porrachia M, Deheyn DD.  2011.  Macrobenthic community response to copper in Shelter Island Yacht Basin, San Diego Bay, California. Marine Pollution Bulletin. 62:701-717.   10.1016/j.marpolbul.2011.01.027   AbstractWebsite

We examined Cu contamination effects on macrobenthic communities and Cu concentration in invertebrates within Shelter Island Yacht Basin, San Diego Bay, California. Results indicate that at some sites, Cu in sediment has exceeded a threshold for "self defense" mechanisms and highlight the potential negative impacts on benthic faunal communities where Cu accumulates and persists in sediments. At sites with elevated Cu levels in sediment, macrobenthic communities were not only less diverse but also their total biomass and body size (individual biomass) were reduced compared to sites with lower Cu. Cu concentration in tissue varied between species and within the same species, reflecting differing abilities to "regulate" their body load. The spatial complexity of Cu effects in a small marina such as SIYB emphasizes that sediment-quality criteria based solely on laboratory experiments should be used with caution, as they do not necessarily reflect the condition at the community and ecosystem levels. (C) 2011 Elsevier Ltd. All rights reserved.

Sellanes, J, Neira C, Quiroga E, Teixido N.  2010.  Diversity patterns along and across the Chilean margin: a continental slope encompassing oxygen gradients and methane seep benthic habitats. Marine Ecology-an Evolutionary Perspective. 31:111-124.   10.1111/j.1439-0485.2009.00332.x   AbstractWebsite

In the present study we review datasets available for the Chilean margin to assess the relationship between environmental (or habitat) heterogeneity and benthic diversity. Several factors, such as the presence of different water masses, including the oxygen-deficient Equatorial Sub-surface Waters (ESSW) at the continental shelf and upper slope, and the Antarctic Intermediate Waters (AIW) at mid slope depths appear to control the bathymetric distribution of benthic communities. The presence of methane seeps and an extended oxygen minimum zone (OMZ) add complexity to the benthic distribution patterns observed. All these factors generate environmental heterogeneity, which is predicted to affect the diversity patterns both along and across the Chilean continental margin. The response to these factors differs among different faunal size groups: meio-, macro-, and megafauna. Physiological adaptations to oxygen deficiency and constraints related to body size of each group seem to explain the larger-scale patterns observed, while sediment/habitat heterogeneity (e.g. at water mass boundaries, hardgrounds, biogeochemical patchiness, sediment organic content, grain size) may influence the local fauna diversity patterns.

Gooday, AJ, Bett BJ, Escobar E, Ingole B, Levin LA, Neira C, Raman AV, Sellanes J.  2010.  Habitat heterogeneity and its influence on benthic biodiversity in oxygen minimum zones. Marine Ecology-an Evolutionary Perspective. 31:125-147.   10.1111/j.1439-0485.2009.00348.x   AbstractWebsite

Oxygen minimum zones (OMZs; midwater regions with O(2) concentrations <0.5 ml l(-1)) are mid-water features that intercept continental margins at bathyal depths (100-1000 m). They are particularly well developed in the Eastern Pacific Ocean, the Arabian Sea and the Bay of Bengal. Based on analyses of data from these regions, we consider (i) how benthic habitat heterogeneity is manifested within OMZs, (ii) which aspects of this heterogeneity exert the greatest influence on alpha and beta diversity within particular OMZs and (iii) how heterogeneity associated with OMZs influences regional (gamma) diversity on continental margins. Sources of sea-floor habitat heterogeneity within OMZs include bottom-water oxygen and sulphide gradients, substratum characteristics, bacterial mats, and variations in the organic matter content of the sediment and pH. On some margins, hard grounds, formed of phosphorites, carbonates or biotic substrata, represent distinct subhabitats colonized by encrusting faunas. Most of the heterogeneity associated with OMZs, however, is created by strong sea-floor oxygen gradients, reinforced by changes in sediment characteristics and organic matter content. For the Pakistan margin, combining these parameters revealed clear environmental and faunal differences between the OMZ core and the upper and lower boundary regions. In all Pacific and Arabian Sea OMZs examined, oxygen appears to be the master driver of alpha and beta diversity in all benthic faunal groups for which data exist, as well as macrofaunal assemblage composition, particularly in the OMZ core. However, other factors, notably organic matter quantity and quality and sediment characteristics, come into play as oxygen concentrations begin to rise. The influence of OMZs on meiofaunal, macrofaunal and megafaunal regional (gamma) diversity is difficult to assess. Hypoxia is associated with a reduction in species richness in all benthic faunal groups, but there is also evidence for endemism in OMZ settings. We conclude that, on balance, OMZs probably enhance regional diversity, particularly in taxa such as Foraminifera, which are more tolerant of hypoxia than others. Over evolutionary timescales, they may promote speciation by creating strong gradients in selective pressures and barriers to gene flow.

Thurber, AR, Kroger K, Neira C, Wiklund H, Levin LA.  2010.  Stable isotope signatures and methane use by New Zealand cold seep benthos. Marine Geology. 272:260-269.   10.1016/j.margeo.2009.06.001   AbstractWebsite

The carbon isotopic composition of seep faunal tissue represents a time-integrated view of the interaction between biology and the biogeochemical gradients within the environment. Here we provide an initial description of carbon and nitrogen stable isotope signatures of dominant symbiont-bearing megafauna and heterotrophic mega- and macrofauna from 10 methane-seep sites on the continental margin of the North Island of New Zealand (662-1201 m water depth). Isotopic signatures suggest that sulfide oxidation supports symbiont-bearing taxa including solemyid and vesicomyid bivalves, and methanotrophic symbionts are present in the seep mussel Bathymodiolus sp Multiple species of Frenulata (Siboglinidae) are present and have a range of isotopic values that are indicative of both thiotroph- and methanotroph-based nutrition. Isotopic composition of the tubeworm Lamellibrachia sp. varied by 23 3 parts per thousand among individuals although there was no consistent difference among sites Variation in methane use by heterotrophic fauna appears to reflect the availability of hard vs. soft substrate, macrofauna on hard substrates had high delta(13)C signatures, reflecting consumption of photosynthetic-derived organic matter Two unique, biotic assemblages were discovered to be fueled largely by methane: a hard-substrate, multi-phyla sponge-associated community (inhabiting the sponge Pseudosuberites sp) and a soft-sediment assemblage dominated by ampharetid polychaetes Isotope signatures yield estimates of 38-100% and 6-100% methane-derived carbon in sponge associates and ampharetid-bed macrofauna. respectively. These estimates are comparable to those made for deeper methane seeps at the Florida Escarpment (3290 m) and Kodiak. Alaska seeps (4445 m) The overall high use of methane as a carbon source by both symbiont-bearing and heterotrophic fauna suggests that New Zealand methane seeps are an ideal model system to study the interaction among metazoans, bacteria, archaea, and their resulting effect on methane cycles. (C) 2009 Elsevier B V All rights reserved

Rathburn, AE, Levin LA, Tryon M, Gieskes JM, Martin JM, Perez ME, Fodrie FJ, Neira C, Fryer GJ, Mendoza G, McMillan PA, Kluesner J, Adamic J, Ziebis W.  2009.  Geological and biological heterogeneity of the Aleutian margin (1965-4822 m). Progress in Oceanography. 80:22-50.   10.1016/j.pocean.2008.12.002   AbstractWebsite

Geological, biological and biogeochemical characterization of the previously unexplored margin off Unimak Island, Alaska between 1965 and 4822 m water depth was conducted to examine: (1) the geological processes that shaped the margin, (2) the linkages between depth, geomorphology and environmental disturbance in structuring benthic communities of varying size classes and (3) the existence, composition and nutritional sources of methane seep biota on this margin. The study area was mapped and sampled using multibeam sonar, a remotely operated vehicle (ROV) and a towed camera system. Our results provide the first characterization of the Aleutian margin mid and lower slope benthic communities (micro-biota, foraminifera, macrofauna and megafauna), recognizing diverse habitats in a variety of settings. Our investigations also revealed that the geologic feature known as the "Ugamak Slide" is not a slide at all, and could not have resulted from a large 1946 earthquake. However, sediment disturbance appears to be a pervasive feature of this margin. We speculate that the deep-sea occurrence of high densities of Elphidium, typically a shallow-water foraminiferan, results from the influence of sediment redeposition from shallower habitats. Strong representation of cumacean, amphipod and tanaid crustaceans among the Unimak macrofauna may also reflect sediment instability. Although some faunal abundances decline with depth, habitat heterogeneity and disturbance generated by canyons and methane seepage appear to influence abundances of biota in ways that supercede any clear depth gradient in organic matter input. Measures of sediment organic matter and pigment content as well as C and N isotopic signatures were highly heterogeneous, although the availability of organic matter and the abundance of microorganisms in the upper sediment (1-5 cm) were positively correlated. We report the first methane seep on the Aleutian slope in the Unimak region (3263-3285 m), comprised of clam bed, pogonophoran field and carbonate habitats. Seep foraminiferal assemblages were dominated by agglutinated taxa, except for habitats above the seafloor on pogonophoran tubes. Numerous infaunal taxa in clam bed and pogonophoran field sediments and deep-sea "reef' cnidarians (e.g., corals and hydroids) residing on rocks near seepage sites exhibited light organic delta(13)C signatures indicative of chemosynthetic nutritional sources. The extensive geological, biogeochemical and biological heterogeneity as well as disturbance features observed on the Aleutian slope provide an attractive explanation for the exceptionally high biodiversity characteristic of the world's continental margins. (C) 2008 Elsevier Ltd. All rights reserved.

Neira, C, Decraemer W.  2009.  Desmotersia levinae, a new genus and new species of free-living nematode from bathyal oxygen minimum zone sediments off Callao, Peru, with discussion on the classification of the genus Richtersia (Chromadorida: Selachinematidae). Organisms Diversity & Evolution. 9:1-2.   10.1016/j.ode.2008.09.004   AbstractWebsite

Desmotersia levinae gen. n., sp. n. is proposed., based on material found in bathyal oxygen minimum zone sediments off the coast of Peru. Desmotersia closely resembles Richtersia in the animals' general appreance and in spiny ornamentation of the body cuticle, but clearly differs in stoma structure and by the presence of a dorsal tooth. Desmotersia levinae is characterized by a variety of spiny ornamentations anteriorly formed by bipartite spines arranged into a fin-like picket fence, by a head with an asymmetrical cephalic capsule, presence of two closely spaced ventral longitudinal rows of copulatory thorns, and by 2-4 ventral thorns in mid-tail positions on the male. As Desmotersia apparently forms a link between Selachinematidae and Desmodoridae, the systematic positions of Desmotersia and Richtersia are discussed. Lis is the :interaction between D. levinae and its habitat, in the full, online edition of this paper. (C) 2008 Gesellschaft fur Biologische Systematik. Published by Elsevier GmbH. All rights reserved.

Grosholz, ED, Levin LA, Tyler AC, Neira C.  2009.  Changes in community structure and ecosystem function following Spartina alterniflora invasion of Pacific estuaries. Human impacts on salt marshes : a global perspective. ( Silliman BR, Grosholz E, Bertness MD, Eds.).:23-40., Berkeley: University of California Press Abstract
Levin, LA, Ekau W, Gooday AJ, Jorissen F, Middelburg JJ, Naqvi SWA, Neira C, Rabalais NN, Zhang J.  2009.  Effects of natural and human-induced hypoxia on coastal benthos. Biogeosciences. 6:2063-2098.   10.5194/bg-6-2063-2009   AbstractWebsite

Coastal hypoxia (defined here as < 1.42 ml L(-1); 62.5 mu M; 2 mg L(-1), approx. 30% oxygen saturation) develops seasonally in many estuaries, fjords, and along open coasts as a result of natural upwelling or from anthropogenic eutrophication induced by riverine nutrient inputs. Permanent hypoxia occurs naturally in some isolated seas and marine basins as well as in open slope oxygen minimum zones. Responses of benthos to hypoxia depend on the duration, predictability, and intensity of oxygen depletion and on whether H(2)S is formed. Under suboxic conditions, large mats of filamentous sulfide oxidizing bacteria cover the seabed and consume sulfide. They are hypothesized to provide a detoxified microhabitat for eukaryotic benthic communities. Calcareous foraminiferans and nematodes are particularly tolerant of low oxygen concentrations and may attain high densities and dominance, often in association with microbial mats. When oxygen is sufficient to support metazoans, small, soft-bodied invertebrates (typically annelids), often with short generation times and elaborate branchial structures, predominate. Large taxa are more sensitive than small taxa to hypoxia. Crustaceans and echinoderms are typically more sensitive to hypoxia, with lower oxygen thresholds, than annelids, sipunculans, molluscs and cnidarians. Mobile fish and shellfish will migrate away from low-oxygen areas. Within a species, early life stages may be more subject to oxygen stress than older life stages. Hypoxia alters both the structure and function of benthic communities, but effects may differ with regional hypoxia history. Human-caused hypoxia is generally linked to eutrophication, and occurs adjacent to watersheds with large populations or agricultural activities. Many occurrences are seasonal, within estuaries, fjords or enclosed seas of the North Atlantic and the NW Pacific Oceans. Benthic faunal responses, elicited at oxygen levels below 2 ml L(-1), typically involve avoidance or mortality of large species and elevated abundances of enrichment opportunists, sometimes prior to population crashes. Areas of low oxygen persist seasonally or continuously beneath upwelling regions, associated with the upper parts of oxygen minimum zones (SE Pacific, W Africa, N Indian Ocean). These have a distribution largely distinct from eutrophic areas and support a resident fauna that is adapted to survive and reproduce at oxygen concentrations < 0.5 ml L(-1). Under both natural and eutrophication-caused hypoxia there is loss of diversity, through attrition of intolerant species and elevated dominance, as well as reductions in body size. These shifts in species composition and diversity yield altered trophic structure, energy flow pathways, and corresponding ecosystem services such as production, organic matter cycling and organic C burial. Increasingly the influences of nature and humans interact to generate or exacerbate hypoxia. A warmer ocean is more stratified, holds less oxygen, and may experience greater advection of oxygen-poor source waters, making new regions subject to hypoxia. Future understanding of benthic responses to hypoxia must be established in the context of global climate change and other human influences such as overfishing, pollution, disease, habitat loss, and species invasions.

Neira, C, Delgadillo-Hinojosa F, Zirino A, Mendoza G, Levin LA, Porrachia M, Deheyn DD.  2009.  Spatial distribution of copper in relation to recreational boating in a California shallow-water basin. Chemistry and Ecology. 25:417-433.   10.1080/02757540903334197   AbstractWebsite

The overall effect of the number of boats on the copper (Cu) levels in the water column and sediment, along with their spatial variability within Shelter Island Yacht Basin (SIYB), San Diego Bay, California was examined. We identified a horizontal gradient of increasing dissolved Cu and Cu in sediment from outside to the head of SIYB which was coincident with the increasing number of boats. Spatial models of Cu distribution in water and sediment indicated the presence of 'hotspots' of Cu concentration. From outside to the head of SIYB, dissolved Cu ranged from 1.3 gL-1 to 14.6 gL-1 in surface water, and 2.0 gL-1 to 10.2 gL-1 in bottom water. Cu in sediment exceeded the Effect Range Low of 34mgkg-1 (i.e. where adverse effects to fauna may occur), with a peak concentration of 442mgkg-1 at the head of the basin. Free Cu++ in surface water was several orders of magnitude higher than in sediment porewater. High-resolution data of Cu species together with probability maps presented in this paper will allow managers to easily visualise and localise areas of impaired quality and to prioritise which areas should be targeted to improve Cu-related conditions.

Sellanes, J, Quiroga E, Neira C.  2008.  Megafauna community structure and trophic relationships at the recently discovered Concepcion Methane Seep Area, Chile, ~36°S. Ices Journal of Marine Science. 65:1102-1111.   10.1093/icesjms/fsn099   AbstractWebsite

The fauna, community composition, and trophic support of the newly discovered Concepcion Methane Seep Area (CMSA) are compared with those at a nearby non-seep control. The assemblage of chemosymbiotic bivalves is defined by eight species, including the families Lucinidae, Thyasiridae, Solemyidae, and Vesicomyidae. Seep polychaetes are represented by Lamellibrachia sp. and two commensal species of the vesicomyid Calyptogena gallardoi. Although taxonomic analysis is still under way, most of the chemosymbiotic species seem to be endemics. The CMSA is a hotspot for non-seep benthic megafauna too; 101 taxa were present, but most of them are colonists or vagrants (i.e. not endemics of methane seeps). Isotope analysis supported the belief that non-symbiont-bearing species utilize photosynthetically fixed carbon, because they were isotopically distinct from the chemosymbiotic bivalve species present. It is our opinion that, at this site, which underlies one of the most productive coastal upwelling regions of the world, spatial heterogeneity and the availability of hard substratum, generated by the presence of authigenic carbonate crusts, are more important factors in attracting non-seep fauna than the availability of locally produced chemosynthetic food.

Neira, C, Levin LA, Grosholz ED, Mendoza G.  2007.  Influence of invasive Spartina growth stages on associated macrofaunal communities. Biological Invasions. 9:975-993.   10.1007/s10530-007-9097-x   AbstractWebsite

In coastal wetlands, invasive plants often act as ecosystem engineers altering flow, light and sediments which, in turn, can affect benthic animal communities. However, the degree of influence of the engineer will vary significantly as it grows, matures and senesces, and surprisingly little is known about how the influence of an ecosystem engineer varies with ontogeny. We address this issue on the tidal flats of San Francisco Bay where hybrid Spartina (foliosa x alterniflora) invaded 30 years ago. The invasion has altered the physico-chemical properties of the sediment habitat, which we predicted should cause changes in macrofaunal community structure and function. Through mensurative and manipulative approaches we investigated the influence of different growth stages of hybrid Spartina on macrobenthos and the underlying mechanisms. Cross-elevation sampling transects were established covering 5 zones (or stages) of the invasion, running from the tidal flat (pre-invasion) to an unvegetated dieback zone. Additionally, we experimentally removed aboveground plant structure in the mature (inner) marsh to mimic the 'unvegetated areas'. Our results revealed four distinct faunal assemblages, which reflected Spartina-induced changes in the corresponding habitat properties along an elevation gradient: a pre-invaded tidal flat, a leading edge of immature invasion, a center of mature invasion, and a senescing dieback area. These stages of hybrid Spartina invasion were accompanied by a substantial reduction in macrofaunal species richness and an increase in dominance, as well as a strong shift in feeding modes, from surface microalgal feeders to subsurface detritus/Spartina feeders (mainly tubificid oligochaetes and capitellid polychaetes). Knowledge of the varying influence of plant invaders on the sediment ecosystem during different phases of invasion is critical for management of coastal wetlands.

Sellanes, J, Quiroga E, Neira C, Gutierrez D.  2007.  Changes of macrobenthos composition under different ENSO cycle conditions on the continental shelf off central Chile. Continental Shelf Research. 27:1002-1016.   10.1016/j.csr.2007.01.001   AbstractWebsite

The course of environmental conditions and shelf macrobenthic communities off Central Chile (similar to 36 degrees S) during the strong 1997-98 El Nino (EN) event is compared with a subsequent and basically "normal" period (2002-2003). Changes in macrofaunal community, feeding mode structure, and biomass size spectra are contrasted over time with changes in oceanographic and sediment settings, in order to assess intra- and inter-annual changes in faunal composition during both ENSO periods. During EN, there was a decrease in biomass and abundance of species known to be well adapted to organic-rich, oxygen-deficient environments, such as the interface-feeding polychacte Paraprionospio pinnata. On the other hand the abundance of highly mobile, burrowing polychaetes remained unaffected, or even increased in biomass. The decline of P. pinnata lasted several years after the demise of warm conditions, possibly due to negative interactions with those more mobile burrowing polychaetes. The percent contribution of subsurface-deposit feeders to total biomass increased during EN (49.3 +/- 12.4% during summer) and declined only in the summer-fall period of 2002-03 (11.1 +/- 4.1%). An opposite trend was observed for interface and surface-deposit feeders. From EN to summer-fall 2002-03 (i.e., normal to low oxygen conditions) the size-structure of the macrobenthos switched from a larger to a smaller-sized assemblage. However, biomass was maintained due to successful recruitment and high abundance of both P. pinnata and the squat lobster, Pleuroncodes monodon. Our results suggest that the shelf macrofaunal community structure exhibit fluctuations at various time scales, and that these changes are more pronounced during and after a strong EN event. In such cases, the effects of such an event may be recorded at latitudes as far south as 36 degrees S, with consequences in the biota lasting for many years after the demise of warm conditions. (c) 2007 Elsevier Ltd. All rights reserved.

Contreras, S, Pantoja S, Neira C, Lange CB.  2007.  Biogeochemistry of surface sediments off Concepcion (~36°S), Chile: El Nino vs. non-El Nino conditions. Progress in Oceanography. 75:576-585.   10.1016/j.pocean.2007.08.030   AbstractWebsite

We compared the signals of several water column properties (upwelling intensity, sea level anomaly, temperature, nutrients, dissolved oxygen, chlorophyll-a, and surface sediments) of the continental shelf off Concepcion (36 degrees S) during the 1997-1998 El Nino with those of a normal year (2002-2003). We found that the primary hydrographic effect of El Nino 1997-1998 was a reduction in the input of nutrient-rich, oxygen-poor Equatorial Subsurface Water over the shelf. This affected the biology of the water column, as evidenced by the reduced phytoplankton biomass. Surface sediment properties (biogenic opal, organic carbon, bulk delta N-15) observed during El Nino 1997-1998 reflected a reduced export production and the sediments failed to show the water column seasonality that occurs under normal conditions. In addition, weakened denitrification and/or upper water column fertilization could be inferred from the sedimentary delta N-15. Although diminished, export production was preserved in the surface sediments, revealing less degraded organic matter in the upwelling period of the El Nino year than in the normal year. We suggest that the fresher organic material on the seafloor was probably associated with a severe reduction in the polychaete Parapronospio pinnata, which is considered to be the most important metazoan remineralizer of organic carbon at the sediment-water interface in the study area. (c) 2007 Elsevier Ltd. All rights reserved.

Sellanes, J, Neira C.  2006.  ENSO as a natural experiment to understand environmental control of meiofaunal community structure. Marine Ecology-an Evolutionary Perspective. 27:31-43.   10.1111/j.1439-0485.2005.00069.x   AbstractWebsite

The sediments of the Bay of Concepcion and the adjacent shelf underlie one of the most productive upwelling areas in the SE Pacific margin. Reports on factors controlling meiofaunal community structure in these kinds of organic-rich and oxygen-deficient habitats are scarce in the literature. In this study, five sites along a transect from the mid-Bay of Concepcion (27 m) to the outer shelf (120 m) were studied on fives dates (May, August, November 1997, and March and May 1998) in order to assess the dynamic relationships between sedimentary organic matter and metazoan meiofauna. The sampling period coincided with the 1997-1998 El Nino event. Sediment parameters investigated were the redox potential discontinuity depth, photosynthetic pigment concentrations (chlorophyll a and phaeopigments), organic carbon, nitrogen, total lipids, carbohydrates, and proteins. In general, lowest values of meiofauna abundance and biomass were found within the naturally eutrophic Bay of Concepcion and towards the shelf break, while maximum values occurred at intermediate depths. During the whole period, the meiofaunal abundance was negatively correlated with the concentration of most of the biochemical components of organic matter, as well as with the sediment phaeopigment content. However, positive correlations were found with chlorophyll a derived indices and with bottom-water oxygen content. Most of the sediment parameters displayed a seasonal cycle, but towards the beginning of 1998, an effect of the 1997-1998 El Nino was evident. Typical austral -summer (i.e. oxygen-deficient) conditions did not develop, and sedimentary parameters reflected a decreased input of phytodetritus. Along the transect, the magnitude of this effect on meiofauna varied among sites. An overall positive response, in terms of meiofaunal abundance was observed, probably due to the amelioration of low oxygen conditions in the sediment.

Levin, LA, Neira C, Grosholz ED.  2006.  Invasive cordgrass modifies wetland trophic function. Ecology. 87:419-432.   10.1890/04-1752   AbstractWebsite

Vascular plants strongly control belowground environments in most ecosystems. Invasion by vascular plants in coastal wetlands, and by cordgrasses (Spartina spp.) in particular, are increasing in incidence globally, with dramatic ecosystem-level consequences. We examined the trophic consequences of' invasion by a Spartina hybrid (S. alterniflora X S. foliosa) in San Francisco Bay (USA) by documenting differences in biomass and trophic structure of benthic communities between sediments invaded by Spartina and uninvaded sediments. We found the invaded system shifted from all algae-bascd to a detritus-based food web. We then tested for a relationship between diet and tolerance to invasion, hypothesizing that species that consume Spartina detritus are more likely to inhabit invaded sediments than those that consume surface algae. Infaunal diets were initially examined with natural abundance stable isotope analyses and application of mixing models, but these yielded an ambiguous picture of food sources. Therefore, we conducted isotopic enrichment experiments by providing N-15-labeled Spartina detritus both on and below the sediment surface in areas that either contained Spartina or were unvegetated. Capitellid and nereid polychaetes, and oligochaetes, groups shown to persist following Spartina invasion of San Francisco Bay tidal flats, took up N-15 from labeled native and invasive Spartina detritus. In contrast, We found that amphipods, bivalves, and other taxa less tolerant to invasion consumed primarily surficial algae, based oil C-13 enrichment experiments. Habitat (Spartina vs. unvegetated patches) and location of' detritus (on or within sediments) did not affect N-15 uptake from cletritus. Our investigations support a "trophic shift" model for ecosystem response to wetland plant invasion and preview loss of key trophic support for fishes and migratory birds by shifting dominance to species not widely consumed by species at higher trophic levels.

Neira, C, Grosholz ED, Levin LA, Blake R.  2006.  Mechanisms generating modification of benthos following tidal flat invasion by a Spartina hybrid. Ecological Applications. 16:1391-1404.   10.1890/1051-0761(2006)016[1391:mgmobf];2   AbstractWebsite

Many coastal habitats are being substantially altered by introduced plants. In San Francisco Bay,, California, USA, a hybrid form of the eastern cordgrass Spartina alterniflora is rapidly invading open mudflats in southern and central sections of the Bay, altering habitat, reducing macrofaunal densities, and shifting species composition. The invasion has resulted in significant losses of surface-feeding amphipods, bivalves, and cirratulid polychaetes, while subsurface feeding groups such as tubificid oligochaetes and capitellid polychaetes have been unaffected. In the present paper, we document the causes and mechanisms underlying the changes observed. Through a series of in situ manipulative experiments we examined the influence of hybrid Spartina canopy on a range of physical, chemical, and biological properties. The hybrid Spartina canopy exerted a strong influence on. the hydrodynamic regime, triggering a series of physical, chemical, and biological changes in the benthic system. Relative to tidal flats, water velocity was reduced in hybrid patches, promoting deposition of fine-grained, organic-rich particles. The resulting changes in the sediment environment included increased porewater sulfide concentrations and anoxia, which led to poor survivorship. of surface feeders such as, bivalves, amphipods, and polychaetes. These are key taxa that support higher trophic levels including migratory shorebirds that feed on tidal flats. Altered flow in the Spartina canopy further contributed to changes in barnacle recruitment and resuspension of adult benthic invertebrates. Increased crab-induced predation pressure associated with Spartina invasion also contributed to changes in benthic invertebrate communities. Our results suggest that multiple physical, chemical, biotic, and trophic impacts of the Spartina invasion have resulted in substantial changes in benthic communities that are likely to have important effects on the entire ecosystem.

Arntz, WE, Gallardo VA, Gutierrez D, Isla E, Levin LA, Mendo J, Neira C, Rowe GT, Tarazona J, Wolff M.  2006.  El Niño and similar perturbation effects on the benthos of the Humboldt, California, and Benguela Current upwelling ecosystems. Advances in Geosciences. 6:243-265.: European Geosciences Union, c/o E.O.S.T. 5, rue Rene Descartes Strasbourg Cedex 67084 France, [], [URL:] AbstractWebsite

To a certain degree, Eastern Boundary Current (EBC) ecosystems are similar: Cold bottom water from moderate depths, rich in nutrients, is transported to the euphotic zone by a combination of trade winds, Coriolis force and Ekman transport. The resultant high primary production fuels a rich secondary production in the upper pelagic and nearshore zones, but where O sub(2) exchange is restricted, it creates oxygen minimum zones (OMZs) at shelf and upper slope (Humboldt and Benguela Current) or slope depths (California Current). These hypoxic zones host a specifically adapted, small macro- and meiofauna together with giant sulphur bacteria that use nitrate to oxydise H sub(2)S. In all EBC, small polychaetes, large nematodes and other opportunistic benthic species have adapted to the hypoxic conditions and co-exist with sulphur bacteria, which seem to be particularly dominant off Peru and Chile. However, a massive reduction of macrobenthos occurs in the core of the OMZ. In the Humboldt Current area the OMZ ranges between <100 and about 600 m, with decreasing thickness in a poleward direction. The OMZ merges into better oxygenated zones towards the deep sea, where large cold-water mega- and macrofauna occupy a dominant role as in the nearshore strip. The Benguela Current OMZ has a similar upper limit but remains shallower. It also hosts giant sulphur bacteria but little is known about the benthic fauna. However, sulphur eruptions and intense hypoxia might preclude the coexistence of significant mega- und macrobenthos. Conversely, off North America the upper limit of the OMZ is considerably deeper (e.g., 500-600 m off California and Oregon), and the lower boundary may exceed 1000m. The properties described are valid for very cold and cold (La Nina and "normal") ENSO conditions with effective upwelling of nutrient-rich bottom water. During warm (El Nino) episodes, warm water masses of low oxygen concentration from oceanic and equatorial regions enter the upwelling zones, bringing a variety of (sub)tropical immigrants. The autochthonous benthic fauna emigrates to deeper water or poleward, or suffers mortality. However, some local macrofaunal species experience important population proliferations, presumably due to improved oxygenation (in the southern hemisphere), higher temperature tolerance, reduced competition or the capability to use different food. Both these negative and positive effects of el Nino influence local artisanal fisheries and the livelihood of coastal populations. In the Humboldt Current system the hypoxic seafloor at outer shelf depths receives important flushing from the equatorial zone, causing havoc on the sulphur bacteria mats and immediate recolonisation of the sediments by mega- and macrofauna. Conversely, off California, the intruding equatorial water masses appear to have lower oxygen than ambient waters, and may cause oxygen deficiency at upper slope depths. Effects of this change have not been studied in detail, although shrimp and other taxa appear to alter their distribution on the continental margin. Other properties and reactions of the two Pacific EBC benthic ecosystems to el Nino seem to differ, too, as does the overall impact of major episodes (e.g., 1982/1983(1984) vs. 1997/1998). The relation of the "Benguela Nino" to ENSO seems unclear although many Pacific- Atlantic ocean and atmosphere teleconnections have been described. Warm, low- oxygen equatorial water seems to be transported into the upwelling area by similar mechanisms as in the Pacific, but most major impacts on the eukaryotic biota obviously come from other, independent perturbations such as an extreme eutrophication of the sediments ensuing in sulphidic eruptions and toxic algal blooms. Similarities and differences of the Humboldt and California Current benthic ecosystems are discussed with particular reference to ENSO impacts since 1972/73. Where there are data available, the authors include the Benguela Current ecosystem as another important, non-Pacific EBC, which also suffers from the effects of hypoxia.

Neira, C, Levin LA, Grosholz ED.  2005.  Benthic macrofaunal communities of three sites in San Francisco Bay invaded by hybrid Spartina, with comparison to uninvaded habitats. Marine Ecology-Progress Series. 292:111-126.   10.3354/meps292111   AbstractWebsite

A hybrid cordgrass, formed from a cross between Spartina alterniflora (Atlantic cordgrass) and S. foliosa (Pacific cordgrass), has recently spread within the intertidal zone of south San Francisco Bay. Sediment properties and macroinfaunal community structure were compared in patches invaded by Spartina hybrid and adjacent uninvaded patches at 3 sites in San Francisco Bay (2 tidal flats and 1 Salicornia marsh). We hypothesized that (1) sediments vegetated by Spartina hybrid would have reduced sediment grain size, higher organic matter content, lower redox potential, lower salinity and reduced microalgal biomass relative to adjacent unvegetated tidal flat sediments, and (2) that differences in the sediment environment would correspond to changes in the infaunal invertebrate community structure and feeding modes. We observed 75 % lower total macro-faunal density and lower species richness in Spartina-vegetated sediments at Elsie Roemer (30 yr old invasion) than in an adjacent unvegetated tidal flat. This was due to lower densities of surface-feeding amphipods, bivalves, cirratulid and spionid polychaetes. The proportional representation of subsurface-deposit feeders was greater in Spartina patches than in unvegetated sediments. At a more recently invaded site (Roberts Landing; 15 yr invasion), Spartina patches differed from tidal flat sediments in composition, but not in abundance. Native (Salicornia) and Spartina patches exhibited similar sediment properties at San Mateo, where the Spartina hybrid invaded 8 to 10 yr earlier. No differences were detected in densities or proportions of surface- or subsurface-deposit feeders, but the proportion of carnivores/omnivores and grazers increased in the hybrid-invaded patches. These studies suggest that the invasive Spartina hybrid in south San Francisco Bay can have differing effects on sediment ecosystems, possibly depending on the location, age, or type of habitats involved.