The importance of vertical and horizontal dimensions of the sediment matrix in structuring nematodes across spatial scales

Intensive surveys have been conducted to unravel spatial patterns of benthic infauna communities. Although it has been recognized that benthic organisms are spatially structured along the horizontal and vertical dimensions of the sediment, little is known on how these two dimensions interact with each other. In this study we investigated the interdependence between the vertical and horizontal dimensions in structuring marine nematodes assemblages. We tested whether the similarity in nematode species composition along the horizontal dimension was dependent on the vertical layer of the sediment. To test this hypothesis, three-cm interval sediment samples (15 cm depth) were taken independently from two bedforms in three estuaries. Results indicated that assemblages living in the top layers are more abundant, species rich and less variable, in terms of species presence/absence and relative abundances, than assemblages living in the deeper layers. Results showed that redox potential explained the greatest amount (12%) of variability in species composition, more than depth or particle size. The fauna inhabiting the more oxygenated layers were more homogeneous across the horizontal scales than those from the reduced layers. In contrast to previous studies, which suggested that reduced layers are characterized by a specific set of tolerant species, the present study showed that species assemblages in the deeper layers are more causal (characterized mainly by vagrant species). The proposed mechanism is that at the superficial oxygenated layers, species have higher chances of being resuspended and displaced over longer distances by passive transport, while at the deeper anoxic layers they are restricted to active dispersal from the above and nearby sediments. Such restriction in the dispersal potential together with the unfavorable environmental conditions leads to randomness in the presence of species resulting in the high variability between assemblages along the horizontal dimension.

Effects of physical disturbance on infaunal and epifaunal assemblages in subtropical, intertidal seagrass beds

We assessed the impact of large-scale commercial and recreational harvesting of polychaete worms Marphysa spp. on macrobenthic assemblages in a subtropical estuary in Queensland, Australia, by examining: (1) the spatial extent of harvesting activities and the rate of recovery of the seagrass habitat over an 18 to 20 mo period; (2) the recovery of infauna in and around commercial pits of known age; (3) the indirect effects of physical disturbance from trampling and deposition of sediments during harvesting on epibenthos in areas adjacent to commercial and recreational pits; (4) impacts of potential indirect effects through manipulative experimentation. Harvesting caused a loss of seagrass, changes to the topography and compaction of the sediments associated with the creation of walls around commercial pits, and the deposition of rubble dug from within the pit. The walls and rubble were still evident after 1.8 to 20 mo, but comprised only a small proportion of the total area on the intertidal banks. There was a shift from an intertidal area dominated by Zostera capricorni to one with a mixture of Z. capricorni, Halophila spp. and Halodule uninervis, but there was no overall decline in the biomass of seagrass in these areas. There were distinct impacts from harvesting on the abundance of benthic infauna, especially amphipods, polychaetes and gastropods, and these effects were still detectable after 4 mo of potential recovery. After 12 me, there were no detectable differences in the abundances of these infauna between dug areas and reference areas, which suggested that infauna had recovered from impacts of harvesting; however, an extensive bloom of toxic fireweed Lyngbya majsucula may have masked any remaining impacts. There were no detectable impacts of harvesting on epifauna living in the seagrass immediately around commercial or recreational pits.

DNA barcoding: an effective tool to overcome morphological identification constraints in the assessment of the ecological quality

DNA barcoding has the potential to overcome taxonomic challenges in biological community assessments. However, fulfilling that potential requires successful amplification of a large and unbiased portion of the community. In this study, we attempted to identify mitochondrial gene cytochrome c oxidase I (COI) barcodes from 1024 benthic invertebrate specimens belonging to 54 taxa from low salinity environments of the Mira estuary and Torgal riverside (SW Portugal). Up to 17 primer pairs and several reaction conditions were attempted among specimens from all taxa, with amplification success defined as a single band of approximately 658 bp visualized on a pre-cast agarose gel, starting near the 5' end of the COI gene and suitable for sequencing. Amplification success was achieved for 99.6% of the 54 taxa, though no single primer was successful for more than 88.9% of the taxa. However, only 68.5% of the specimens within these taxa successfully amplified. Inhibition factors resulting from a non-purified DNA extracted and inexistence of species-specific primers for COI were pointed as the main reasons for an unsuccessful amplification. These results suggest that DNA barcoding can be an effective tool for application in low salinity environments where taxa such as chironomids and oligochaetes are challenging for morphological identification. Nevertheless, its implementation is not simple, as methods are still being standardized and multiple species

Effects of a large fishing closure on benthic communities in the western Gulf of Maine: recovery from the effects of gillnets and otter trawls

The recovery of benthic communities inside the western Gulf of Maine fishing closure area was evaluated by comparing invertebrate assemblages at sites inside and outside of the closure four to six years after the closure was established. The major restriction imposed by the closure was a year-round prohibition of bottom gillnets and otter trawls. A total of 163 seafloor sites (~half inside and half outside the closure) within a 515-km2 study area were sampled with some combination of Shipek grab, Wildco box corer, or underwater video. Bottom types ranged from mud (silt and clay) to boulders, and the effects of the closure on univariate measures (total density, biomass, taxonomic richness) of benthos varied widely among sediment types. For sites with predominantly mud sediments, there were mixed effects on inside and outside infauna and no effect on epifauna. For sites with mainly sand sediments, there were higher density, biomass, and taxonomic richness for infauna inside the closure, but no significant effects on epifauna. For sites dominated by gravel (which included boulders in some areas), there were no effects on infauna but strong effects on epifaunal density and taxonomic richness. For fishing gear, the data indicated that infauna recovered in sand from the impacts of otter trawls operated inside the closure but that they did not recover in mud, and that epifauna recovered on gravel bottoms from the impact of gillnets used inside the closure. The magnitudes of impact and recovery, however, cannot be inferred directly from our data because of a confounding factor of different fishing intensities outside the closure for a direct comparison of preclosure and postclosure data. The overall negative impact of trawls is likely underestimated by our data, whereas the negative impact of gillnets is likely overestimated.

Benthic foraminiferal distribution on the southeastern Brazilian shelf and upper slope

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Benthic foraminiferal distribution on the southeastern Brazilian shelf and upper slope

Foraminiferal data were obtained from 66 samples of box cores on the southeastern Brazilian upper margin (between 23.8A degrees-25.9A degrees S and 42.8A degrees-46.13A degrees W) to evaluate the benthic foraminiferal fauna distribution and its relation to some selected abiotic parameters. We focused on areas with different primary production regimes on the southern Brazilian margin, which is generally considered as an oligotrophic region. The total density (D), richness (R), mean diversity (H) over bar`, average living depth (ALD(X) ) and percentages of specimens of different microhabitats (epifauna, shallow infauna, intermediate infauna and deep infauna) were analyzed. The dominant species identified were Uvigerina spp., Globocassidulina subglobosa, Bulimina marginata, Adercotryma wrighti, Islandiella norcrossi, Rhizammina spp. and Brizalina sp.. We also established a set of mathematical functions for analyzing the vertical foraminiferal distribution patterns, providing a quantitative tool that allows correlating the microfaunal density distributions with abiotic factors. In general, the cores that fit with pure exponential decaying functions were related to the oligotrophic conditions prevalent on the Brazilian margin and to the flow of the Brazilian Current (BC). Different foraminiferal responses were identified in cores located in higher productivity zones, such as the northern and the southern region of the study area, where high percentages of infauna were encountered in these cores, and the functions used to fit these profiles differ appreciably from a pure exponential function, as a response of the significant living fauna in deeper layers of the sediment. One of the main factors supporting the different foraminiferal assemblage responses may be related to the differences in primary productivity of the water column and, consequently, in the estimated carbon flux to the sea floor. Nevertheless, also bottom water velocities, substrate type and water depth need to be considered.

Benthic foraminifera in surface sediments of the Gulf of Lions

Surface sediment was sampled at two bathyal sites in the southwestern Gulf of Lions in the western Mediterranean Sea in February and August 1997 to study the distribution and microhabitat of living (Rose Bengal stained) deep sea benthic foraminifera. Both standing stock and diversity of the faunas, and the microhabitat of distinct species mirror the trophic situation and the depth of the oxidised layer at the different sites. Our results suggest that the faunas do not comprise highly opportunistic species and are adapted to rather stable environments. In the axial channel of the Lacaze-Duthiers Canyon, organic matter fluxes are enhanced due to advective transport of organic matter resulting in elevated oxygen consumption rates in the surface sediment and a rather thin oxidised layer. The corresponding benthic foraminiferal fauna is characterised by rather high standing stock and diversity, and a well-developed deep infauna. In addition to freshly deposited phytodetritus, more degraded organic matter seems to be an important food source. In contrast, at the open slope, organic matter fluxes and oxygen consumption rates in the surface sediment are lower and the oxidised layer is much thicker than inside the canyon. The corresponding benthic foraminiferal fauna comprises mainly epifaunal and shallow-infaunal species with much lower standing stocks and clear differences between February and August. In August standing stocks are higher and the average living depths of most species shift towards the sediment surface. These differences can be attributed to patchiness or represent a seasonal trophic signal.

Response of deep-sea benthic foraminifera to Late Quaternary climate changes, southeast Indian Ocean, offshore Western Australia

The Late Quaternary benthic foraminifera of four deep-sea cores off Western Australia (ODP 122-760A, ODP 122-762B, BMR96GC21 and RC9-150) have been examined for evidence of increased surface productivity to explain the anomalously low sea-surface paleotemperatures inferred by planktic foraminifera for the last and penultimate glaciations. The delta13C trends of Cibicidoides wuellerstorfi, and differences between the delta13C trends of planktics (Globigerinoides sacculifer) and benthics (C. wuellerstorfi) in the four cores indicate that during stage 6 bottom waters were significantly depleted in delta13C, and strong delta13C gradients were established in the water column, while during stage 2 and the Last Glacial Maximum, delta13C trends did not differ greatly from that of the Holocene. Two main assemblages of benthic foraminifera were identified by principal component analyses: one dominated by Uvigerina peregrina, another dominated by U. proboscidea. Abundance of these Uvigerinids, and of taxa preferring an infaunal microhabitat, and of Epistominella exigua and Bulimina aculeata indicate that episodes of high influx of particulate organic matter were established in most sites during glacial episodes, and particularly so during stage 6, while evidence for upwelling during the Last Glacial Maximum is less strong. The Penultimate Glaciation upwellings were established within the areas of low sea-surface paleotemperature indicated by planktic foraminifera. During the Last Interglacial Climax, upwelling appears to have been established in an isolated region offshore from a strengthened Leeuwin Current off North West Cape. Last Glacial Maximum delta13C values of C. wuellerstorfi at waterdepths of less than 2000 m show smaller than global mean glacial-interglacial changes suggesting the development of a deep hydrological front. A similar vertical stratification/bathyal front was also established during the Penultimate Glaciation.

Mineralogy, geochemistry and benthic foraminifera of the Gorrondatxe beach section

A distinctive low-carbonate interval interrupts the continuous limestone-marl alternation of the deep-marine Gorrondatxe section at the early Lutetian (middle Eocene) C21r/C21n Chron transition. The interval is characterized by increased abundance of turbidites and kaolinite, a 3 per mil decline in the bulk d13C record, a >1 per mil decline in benthic foraminiferal d13C followed by a gradual recovery, a distinct deterioration in foraminiferal preservation, high proportions of warm-water planktic foraminifera and opportunistic benthic foraminifera, and reduced trace fossil and benthic foraminiferal diversity, thus recording a significant environmental perturbation. The onset of the perturbation correlates with the C21r-H6 event recently defined in the Atlantic and Pacific oceans, which caused a 2°C warming of the seafloor and increased carbonate dissolution. The perturbation was likely caused by the input of 13C-depleted carbon into the ocean-atmosphere system, thus presenting many of the hallmarks of Paleogene hyperthermal deposits. However, from the available data it is not possible to conclusively state that the event was associated with extreme global warming. Based on our analysis, the perturbation lasted 226 kyr, from 47.44 to 47.214 Ma, and although this duration suggests that the triggering mechanism may have been similar to that of the Paleocene-Eocene Thermal Maximum (PETM), the magnitude of the carbon input and the subsequent environmental perturbation during the early Lutetian event were not as severe as in the PETM.

Foraminifer, epifauna and infauna abundance of ODP Hole 183-1138A and core ELT54.007-PC, Kerguelen Plateau

Late Campanian and Maastrichtian benthic foraminifers are recorded from 12 samples from Ocean Drilling Program (ODP) Leg 183, Cores 183-1138A-52R through 63R (487.3-602.4 meters below seafloor), Kerguelen Plateau, Indian Ocean, and Danian benthics from one sample in the same section. The entire late Maastrichtian foraminifer fauna is noted from a dredge sample 220 km to the north. The structure of the fauna is compared with the Cenomanian-Turonian of the nearby Eltanin core E54-7. Faunas are reviewed in terms of planktonic percentage, composition, epifaunal/infaunal ratios, and dominance/diversity indices. The region was in the cool Austral Faunal Province through the Campanian-Maastrichtian and was probably warmer in the Cenomanian-Turonian. The ODP section is now 1600 meters below sea level and has subsided several hundred meters since deposition. Its fauna is dominated by epifaunal species suggesting little influence of upwelling. The dredge location has subsided little. Its fauna has a high infaunal content consistent with significant influence of upwelling near the plateau edge. The dominant benthic species remain constant through the ODP Cretaceous section, but subdominance changes, and the section is divided into three informal zones based on dominance/subdominance characteristics of the benthic fauna. Brief taxonomic comments are made on several species and some are figured.

Benthic foraminifera of the central Indian Ocean

Late Oligocene to late Pliocene vertical water-mass stratification along depth traverses in the northern Indian Ocean is depicted in this paper by benthic foraminifer index faunas. During most of this time, benthic faunas indicate well-oxygenated, bottom-water conditions at all depths except under the southern Indian upwelling and in the Pliocene in the southern Arabian Sea. Faunas suggest the initiation of lower oxygen conditions at intermediate depths in the northern Indian Ocean beginning in Oligocene Zone P21a. Lower oxygen conditions intensified during primary productivity pulses, possibly related to increased upwelling vigor, in the latest Oligocene and throughout most of the late middle through late Miocene. During times of elevated primary production, there may be more oxygen flux into sedimentary pore waters and the shallow infaunal habitat may become more oxygenated. One criterion for locating the source of "new" water masses is vertical homogeneity of benthic foraminifer indexes for well-oxygenated water masses from intermediate through abyssal depths. In the northern Mascarene Basin, this type of faunal homogeneity with depth corroborates the proposal that the northern Indian Ocean was an area of sinking well-oxygenated waters through most of the Miocene before Zone N17. Oxygenated, possibly "new" intermediate-water masses in the low- to middle-latitude Mascarene and Central Indian basins first developed in the late Oligocene. These well-oxygenated waters were probably more fertile than the Antarctic Intermediate Waters (AAIW) that cover intermediate depths in these areas today. Production of intermediate waters more similar to modern AAIW is indicated by the sparse benthic population of epifaunal rotaloid species in the northern Mascarene Basin during middle Miocene Zone N9 and from early through late Pliocene time. Deep-water characteristics are more difficult to interpret because of the extensive redeposition at the deeper sites. Redeposited intermediate, rather than shallow, water fossils and erosion from north to south in the Mascarene Basin are incompatible with the sluggish circulation from south to north through the western Indian Ocean basins today. Such erosion could result from the vigorous sinking of an intermediate-depth water mass of northern origin. Before late Oligocene Zone P22, benthic faunas indicate a twofold subdivision of the troposphere, with the boundary between upper and lower well-oxygenated water masses located from 2500-3000 mbsl. No characteristic bottom-water fauna developed before the end of late Oligocene Zone P22. Deep and abyssal benthic indexes suggest the development of water masses similar to those of the present day in the latest Miocene. Faunas containing deep-water benthic indexes, including the uvigerinids, suggestive of a water mass similar to modern Indian Deep Water (IDW), appeared during the late Miocene in the northern Mascarene and Central Indian basins. In the early Pliocene, this deep-water fauna was found only in the Central Indian Basin, whereas a fauna typical of modern Antarctic Bottom Water (AABW) spread through deep waters at 2800 mbsl in the Mascarene Basin. By late Pliocene Zone N21, however, deep-water faunas similar to their modern analogs were developed in both the eastern and western basins. Abyssal faunas, studied only in the Mascarene Basin, show more or less similarity to those under modern AABW. Bottom-water faunas containing Nuttallides umbonifera or Epistominella exiguua were first differentiated at the end of Zone P22, then appeared episodically during the early Miocene. These AABW-type faunas reappeared and migrated updepth into deep waters during the glacial episodes at the end of the Miocene and at the beginning of the Pliocene. By late Pliocene Zone N21, however, a bottom-water fauna similar to that under eastern Indian Bottom Water (IBW) developed in the Mascarene Basin. Modern bottom-water characteristics of the Mascarene Basin must have developed after ZoneN21.

Stable oxygen isotope records of different benthic foraminiferal species of core GeoB3004-1 from the western Arabian Sea

The stable isotope composition of one epifaunal and three infaunal benthic foraminiferal species of a sediment core from 1800 m water depth of the western Arabian Sea was determined to evaluate deepwater oxygenation, organic matter remineralization, and early diagenetic processes during the past 190,000 years. The d18O records reveal species-specific metabolic effects, susceptibility to changes in carbonate ion concentration, and supralysoclinal calcite dissolution. The foraminiferal d13C records reveal changes in the stable carbon isotope gradients of pore water dissolved inorganic carbon (d13CDIC) and in the microhabitat depth of infaunal species. Maximum d13CDIC offsets between bottom and pore waters ranged between mean values of 0.8 and 1.2% corresponding to estimates of deepwater oxygen concentration between approximately 1 and 2.7 ml/l. Intervals of improved deepwater oxygenation coincided with high benthic foraminiferal diversity and indicate the admixture of well-oxygenated deepwater masses during interglacials. During interglacial maxima the d13C difference between epifauna and shallow infauna indicates highest organic matter remineralization rates at times of maximum organic matter fluxes.

Communities and microhabitats of living benthic foraminifera from the tropical East Atlantic

Living (Rose Bengal stained) benthic foraminifera were collected with a multicorer from six stations between 2°N and 12°S off West Africa. The foraminiferal communities in the investigated area reflect the direct influence of different productivity regimes, and are characterized by spatially and seasonally varying upwelling activity. At five stations, foraminiferal abundance coincides well with the gradient of surface productivity. However, at one station off the Congo River, the influence of strong fresh water discharge is documented. Although this station lies directly in the center of an upwelling area, foraminiferal standing stocks are surprisingly low. It is suggested that the Congo discharge may induce a fractionation of the organic matter into small and light particles of low nutritional content, by contrast to the relatively fast-sinking aggregates found in the centers of high productivity areas. Quality and quantity of the organic matter seem to influence the distribution of microhabitats as well. The flux of organic carbon to the sea-floor controls the sequence of degradation of organic matter in sediment and the position of different redox fronts. The vertical foraminiferal stratification within sediment closely parallels the distribution of oxygen and nitrate in porewater, and reflects different nutritive strategies and adaptation to different types of organic matter. The epifauna and shallow infauna colonize oxygenated sediments where labile organic matter is available. The intermediate infauna (M. barleeanum) is linked to the zone of nitrate reduction in sediments where epifaunal and shallow infaunal species are not competitive anymore, and must feed on bacterial biomass or on metabolizable nutritious particles produced by bacterial degradation of more refractory organic matter. The deep infauna shows its maximum distribution in anoxic sediments, where no easily metabolizable organic matter is available.

Benthic foraminiferal distribution on the southeastern Brazilian shelf and upper slope

Foraminiferal data were obtained from 66 samples of box cores on the southeastern Brazilian upper margin (between 23.8A degrees-25.9A degrees S and 42.8A degrees-46.13A degrees W) to evaluate the benthic foraminiferal fauna distribution and its relation to some selected abiotic parameters. We focused on areas with different primary production regimes on the southern Brazilian margin, which is generally considered as an oligotrophic region. The total density (D), richness (R), mean diversity (H) over bar', average living depth (ALD(X) ) and percentages of specimens of different microhabitats (epifauna, shallow infauna, intermediate infauna and deep infauna) were analyzed. The dominant species identified were Uvigerina spp., Globocassidulina subglobosa, Bulimina marginata, Adercotryma wrighti, Islandiella norcrossi, Rhizammina spp. and Brizalina sp.. We also established a set of mathematical functions for analyzing the vertical foraminiferal distribution patterns, providing a quantitative tool that allows correlating the microfaunal density distributions with abiotic factors. In general, the cores that fit with pure exponential decaying functions were related to the oligotrophic conditions prevalent on the Brazilian margin and to the flow of the Brazilian Current (BC). Different foraminiferal responses were identified in cores located in higher productivity zones, such as the northern and the southern region of the study area, where high percentages of infauna were encountered in these cores, and the functions used to fit these profiles differ appreciably from a pure exponential function, as a response of the significant living fauna in deeper layers of the sediment. One of the main factors supporting the different foraminiferal assemblage responses may be related to the differences in primary productivity of the water column and, consequently, in the estimated carbon flux to the sea floor. Nevertheless, also bottom water velocities, substrate type and water depth need to be considered.