Shifts in the microbial community structure in different temperatures during sample storage from IODP Hole 325-M0058A

The objective of this study was to determine shifts in the microbial community structure and potential function based on standard Integrated Ocean Drilling Program (IODP) storage procedures for sediment cores. Standard long-term storage protocols maintain sediment temperature at 4°C for mineralogy, geochemical, and/or geotechnical analysis whereas standard microbiological sampling immediately preserves sediments at -80°C. Storage at 4°C does not take into account populations may remain active over geologic time scales at temperatures similar to storage conditions. Identification of active populations within the stored core would suggest geochemical and geophysical conditions within the core change over time. To test this potential, the metabolically active fraction of the total microbial community was characterized from IODP Expedition 325 Great Barrier Reef sediment cores prior to and following a 3-month storage period. Total RNA was extracted from complementary 2, 20, and 40 m below sea floor sediment samples, reverse transcribed to complementary DNA and then sequenced using 454 FLX sequencing technology, yielding over 14,800 sequences from the six samples. Interestingly, 97.3% of the sequences detected were associated with lineages that changed in detection frequency during the storage period including key biogeochemically relevant lineages associated with nitrogen, iron, and sulfur cycling. These lineages have the potential to permanently alter the physical and chemical characteristics of the sediment promoting misleading conclusions about the in situ biogeochemical environment. In addition, the detection of new lineages after storage increases the potential for a wider range of viable lineages within the subsurface that may be underestimated during standard community characterizations.

Effects of elevated CO2 and temperature on an intertidal meiobenthic community

In the near future, the marine environment is likely to be subjected to simultaneous increases in temperature and decreased pH. The potential effects of these changes on intertidal, meiofaunal assemblages were investigated using a mesocosm experiment. Artificial Substrate Units containing meiofauna from the extreme low intertidal zone were exposed for 60 days to eight experimental treatments (four replicates for each treatment) comprising four pH levels: 8.0 (ambient control), 7.7 & 7.3 (predicted changes associated with ocean acidification), and 6.7 (CO2 point-source leakage from geological storage), crossed with two temperatures: 12 °C (ambient control) and 16 °C (predicted). Community structure, measured using major meiofauna taxa was significantly affected by pH and temperature. Copepods and copepodites showed the greatest decline in abundance in response to low pH and elevated temperature. Nematodes increased in abundance in response to low pH and temperature rise, possibly caused by decreased predation and competition for food owing to the declining macrofauna density. Nematode species composition changed significantly between the different treatments, and was affected by both seawater acidification and warming. Estimated nematode species diversity, species evenness, and the maturity index, were substantially lower at 16 °C, whereas trophic diversity was slightly higher at 16 °C except at pH 6.7. This study has demonstrated that the combination of elevated levels of CO2 and ocean warming may have substantial effects on structural and functional characteristics of meiofaunal and nematode communities, and that single stressor experiments are unlikely to encompass the complexity of abiotic and biotic interactions. At the same time, ecological interactions may lead to complex community responses to pH and temperature changes in the interstitial environment.

Seawater carbonate chemistry in Hog reef and calcification rate in the Bermuda reef community, 2010

Despite the potential impact of ocean acidification on ecosystems such as coral reefs, surprisingly, there is very limited field data on the relationships between calcification and seawater carbonate chemistry. In this study, contemporaneous in situ datasets of seawater carbonate chemistry and calcification rates from the high-latitude coral reef of Bermuda over annual timescales provide a framework for investigating the present and future potential impact of rising carbon dioxide (CO2) levels and ocean acidification on coral reef ecosystems in their natural environment. A strong correlation was found between the in situ rates of calcification for the major framework building coral species Diploria labyrinthiformis and the seasonal variability of [CO32-] and aragonite saturation state omega aragonite, rather than other environmental factors such as light and temperature. These field observations provide sufficient data to hypothesize that there is a seasonal "Carbonate Chemistry Coral Reef Ecosystem Feedback" (CREF hypothesis) between the primary components of the reef ecosystem (i.e., scleractinian hard corals and macroalgae) and seawater carbonate chemistry. In early summer, strong net autotrophy from benthic components of the reef system enhance [CO32-] and omega aragonite conditions, and rates of coral calcification due to the photosynthetic uptake of CO2. In late summer, rates of coral calcification are suppressed by release of CO2 from reef metabolism during a period of strong net heterotrophy. It is likely that this seasonal CREF mechanism is present in other tropical reefs although attenuated compared to high-latitude reefs such as Bermuda. Due to lower annual mean surface seawater [CO32-] and omega aragonite in Bermuda compared to tropical regions, we anticipate that Bermuda corals will experience seasonal periods of zero net calcification within the next decade at [CO32-] and omega aragonite thresholds of ~184 micro moles kg-1 and 2.65. However, net autotrophy of the reef during winter and spring (as part of the CREF hypothesis) may delay the onset of zero NEC or decalcification going forward by enhancing [CO32-] and omega aragonite. The Bermuda coral reef is one of the first responders to the negative impacts of ocean acidification, and we estimate that calcification rates for D. labyrinthiformis have declined by >50% compared to pre-industrial times.

Response of benthic foraminifera to ocean acidification in their natural sediment environment: a long-term culturing experiment

Calcifying foraminifera are expected to be endangered by ocean acidification; however, the response of a complete community kept in natural sediment and over multiple generations under controlled laboratory conditions has not been constrained to date. During 6 months of incubation, foraminiferal assemblages were kept and treated in natural sediment with pCO2-enriched seawater of 430, 907, 1865 and 3247 µatm pCO2. The fauna was dominated by Ammonia aomoriensis and Elphidium species, whereas agglutinated species were rare. After 6 months of incubation, pore water alkalinity was much higher in comparison to the overlying seawater. Consequently, the saturation state of Omega calc was much higher in the sediment than in the water column in nearly all pCO2 treatments and remained close to saturation. As a result, the life cycle (population density, growth and reproduction) of living assemblages varied markedly during the experimental period, but was largely unaffected by the pCO2 treatments applied. According to the size-frequency distribution, we conclude that foraminifera start reproduction at a diameter of 250 µm. Mortality of living Ammonia aomoriensis was unaffected, whereas size of large and dead tests decreased with elevated pCO2 from 285 µm (pCO2 from 430 to 1865 µatm) to 258 µm (pCO2 3247 µatm). The total organic content of living Ammonia aomoriensis has been determined to be 4.3% of CaCO3 weight. Living individuals had a calcium carbonate production rate of 0.47 g/m**2/a, whereas dead empty tests accumulated a rate of 0.27 g /m**2/a. Although Omega calc was close to 1, approximately 30% of the empty tests of Ammonia aomoriensis showed dissolution features at high pCO2 of 3247 µatm during the last 2 months of incubation. In contrast, tests of the subdominant species, Elphidium incertum, stayed intact. Our results emphasize that the sensitivity to ocean acidification of the endobenthic foraminifera Ammonia aomoriensis in their natural sediment habitat is much lower compared to the experimental response of specimens isolated from the sediment.

Seawater carbonate chemistry and community calcification during Miyako Island (Japan) coral reef studies, 1994

Coral reefs are characterized by enormous carbonate production of the organisms. It is known that rapid calcification is linked to photosynthesis under control of the carbonate equilibrium in seawater. We have established a model simulating the coexisting states of photosynthesis and calcification in order to examine the effects of photosynthesis and calcification on the carbonate system in seawater. Supposing that the rates of photosynthesis and calcification are proportional to concentrations of their inorganic carbon source, the model calculations indicate that three kinds of unique interactions of the organic and inorganic carbon productions are expected. These are photosynthetic enhancement of calcification, calcification which benefits photosynthesis and carbonate dissolution induced by respiration. The first effect appears when the photosynthetic rate is more than approximately 1.2 larger than that of calcification. This effect is caused by the increase of CO3 content and carbonate saturation degree in seawater. If photosynthesis use molecular carbon dioxide, the second effect occurs when the calcification rate is more than approximately 1.6 times larger than that of photosynthesis. Time series model experiments indicate that photosynthesis and calcification potentially enhance each other and that organic and inorganic carbon is produced more efficiently in the coexisting system than in the isolated reactions. These coexisting effects on production enhancement of photosynthesis and calcification are expected to appear not only in the internal pool of organisms but also in a reef environment which is isolated from the outer ocean during low tide. According to the measurements on the fringing type Shiraho Reef in the Ryukyu Islands, the diurnal change of water properties (pH, total alkalinity, total carbon dioxide and carbonate saturation degree) were conspicuous. This environment offers an appropriate condition for the appearance of these coexisting effects. The photosynthetic enhancement of calcification and the respiratory inducement of decalcification were observed during day-time and night-time slack-water periods, respectively. These coexisting effects, especially the photosynthetic enhancement of calcification, appear to play important roles for fluorishing coral reef communities.

Seawater carbonate chemistry and calcification rate in the Bermuda reef community, 2010

Despite the potential impact of ocean acidification on ecosystems such as coral reefs, surprisingly, there is very limited field data on the relationships between calcification and seawater carbonate chemistry. In this study, contemporaneous in situ datasets of seawater carbonate chemistry and calcification rates from the high-latitude coral reef of Bermuda over annual timescales provide a framework for investigating the present and future potential impact of rising carbon dioxide (CO2) levels and ocean acidification on coral reef ecosystems in their natural environment. A strong correlation was found between the in situ rates of calcification for the major framework building coral species Diploria labyrinthiformis and the seasonal variability of [CO32-] and aragonite saturation state omega aragonite, rather than other environmental factors such as light and temperature. These field observations provide sufficient data to hypothesize that there is a seasonal "Carbonate Chemistry Coral Reef Ecosystem Feedback" (CREF hypothesis) between the primary components of the reef ecosystem (i.e., scleractinian hard corals and macroalgae) and seawater carbonate chemistry. In early summer, strong net autotrophy from benthic components of the reef system enhance [CO32-] and omega aragonite conditions, and rates of coral calcification due to the photosynthetic uptake of CO2. In late summer, rates of coral calcification are suppressed by release of CO2 from reef metabolism during a period of strong net heterotrophy. It is likely that this seasonal CREF mechanism is present in other tropical reefs although attenuated compared to high-latitude reefs such as Bermuda. Due to lower annual mean surface seawater [CO32-] and omega aragonite in Bermuda compared to tropical regions, we anticipate that Bermuda corals will experience seasonal periods of zero net calcification within the next decade at [CO32-] and omega aragonite thresholds of ~184 micro moles kg-1 and 2.65. However, net autotrophy of the reef during winter and spring (as part of the CREF hypothesis) may delay the onset of zero NEC or decalcification going forward by enhancing [CO32-] and omega aragonite. The Bermuda coral reef is one of the first responders to the negative impacts of ocean acidification, and we estimate that calcification rates for D. labyrinthiformis have declined by >50% compared to pre-industrial times.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Seawater carbonate chemistry in Hog reef, Bermuda reef community, 2010

Despite the potential impact of ocean acidification on ecosystems such as coral reefs, surprisingly, there is very limited field data on the relationships between calcification and seawater carbonate chemistry. In this study, contemporaneous in situ datasets of seawater carbonate chemistry and calcification rates from the high-latitude coral reef of Bermuda over annual timescales provide a framework for investigating the present and future potential impact of rising carbon dioxide (CO2) levels and ocean acidification on coral reef ecosystems in their natural environment. A strong correlation was found between the in situ rates of calcification for the major framework building coral species Diploria labyrinthiformis and the seasonal variability of [CO32-] and aragonite saturation state omega aragonite, rather than other environmental factors such as light and temperature. These field observations provide sufficient data to hypothesize that there is a seasonal "Carbonate Chemistry Coral Reef Ecosystem Feedback" (CREF hypothesis) between the primary components of the reef ecosystem (i.e., scleractinian hard corals and macroalgae) and seawater carbonate chemistry. In early summer, strong net autotrophy from benthic components of the reef system enhance [CO32-] and omega aragonite conditions, and rates of coral calcification due to the photosynthetic uptake of CO2. In late summer, rates of coral calcification are suppressed by release of CO2 from reef metabolism during a period of strong net heterotrophy. It is likely that this seasonal CREF mechanism is present in other tropical reefs although attenuated compared to high-latitude reefs such as Bermuda. Due to lower annual mean surface seawater [CO32-] and omega aragonite in Bermuda compared to tropical regions, we anticipate that Bermuda corals will experience seasonal periods of zero net calcification within the next decade at [CO32-] and omega aragonite thresholds of ~184 micro moles kg-1 and 2.65. However, net autotrophy of the reef during winter and spring (as part of the CREF hypothesis) may delay the onset of zero NEC or decalcification going forward by enhancing [CO32-] and omega aragonite. The Bermuda coral reef is one of the first responders to the negative impacts of ocean acidification, and we estimate that calcification rates for D. labyrinthiformis have declined by >50% compared to pre-industrial times.

Meiofauna and the structure of the benthic community in the Iberian deep sea basin

1. On the cruises 3 and 15 of R.V. "Meteor" 6 grab samples, and 6 hauls with the 6 m Agassiztrawl were taken and at 2 stations the deep sea camera was lowered. This material gave quantitative results on the meiofauna and minimum counts of the macrofauna. 2. The nematodes constitute nearly 95% of the meiofauna, the copepoda only 2%. With increasing sediment depth the density of animals decrease gradually. In the uppermost centimeter of sediment 42.6% of the meiofauna are found while only 3.7% live in layer 6-7 cm. Meiofauna weight ranges from 0.6-5.7 mg/25 m**2 surface i.e. 0.24-2.8 g/m**2. 3. Mean numbers of individuals and weights show standard errors of 20-30 %. As an approximate average values for further considerations the weight of the meiofauna in the area was taken as 1 g/m**2 4. Quantitative information on the macrofauna is derived from the trawls and the photographs for the actinia Chitonanthus abyssorum only, which is found in the rate of 1 individual/36-72 m**2, but seems to be less abundant generally. 5. Animal density does not decrease steadily from nearshore to offshore biocoenoses, i.e. generally with increasing depth. The decrease is more pronounced for macro- than for meiofauna. For the deep sea the weight proportion of macrofauna : meiofauna is of the order of 1 : 1. 6. With the assumption, that adaptation of metabolism to deep sea conditions is similar in macro- and meiofauna total metabolism of invertebrates is ascribed to meiofauna to more than 80%. 7. The structure of the biocoenosis of the deep sea floor is characterized by the meiofauna living on and in the sediment and by the dominance of sediment feeders in the macrofauna. 8. Considering the large numbets and high partition rates of bacteria a comparative large part of the metabolism in the deep sea sediment must be ascribed to bacteria. This favours the hypothesis, that with increasing depth and decreasing addition of organic material to the sediment, the importance of meiofauna and microorganisms for total metabolism increases. 9. Considering the different modes of food transport to the deep sea environment, i.e. sinking of dead particles, transport by vertical migration of organisms, aggregation of organic particles, adsorption of dissoloved organic substance to inorganic particles, and heterotrophy, the sediment may be assumed to contain more food for invertebrates than the water above the bottom. 10. Suspensions feeders of macrofauna are fixed to hard substrates in the sediment surface. Some of them are shown to bend themselves down to the bottom in underwater photographs. This suggests the idea that some deep sea suspension feeders partly depend on food from the sediment surface, on which they feed directly.

Seawater carbonate chemistry and community calcification near Lizar Island, 2011

It is predicted that surface ocean pH will reach 7.9, possibly 7.8 by the end of this century due to increased carbon dioxide (CO2) in the atmosphere and in the surface ocean. While aragonite-rich sediments don't begin to dissolve until a threshold pH of ~ 7.8 is reached, dissolution from high-Mg calcites is evident with any drop in pH. Indeed, it is high-Mg calcite that dominates the reaction of carbonate sediments with increased CO2, which undergoes a rapid neomorphism process to a more stable, low-Mg calcite. This has major implications for the future of the high-Mg calcite producing organisms within coral reef ecosystems. In order to understand any potential buffering system offered by the dissolution of carbonate sediments under a lower oceanic pH, this process of high-Mg calcite dissolution in the reef environment must be further elucidated.