Relative significance of pelagic, benthic and allochthonous organic matter to microbial carbon cycling in a phosphorus-depleted subtropical estuary (Florida Bay)

Heterotrophic bacteria are important decomposers and transformers of primary production and provide an important link between detritus and the aquatic food web. In seagrass ecosystems, much of seagrass primary production is unavailable through direct grazing and must undergo microbial reworking before seagrass production can enter the aquatic food web. The goal of my dissertation research is to understand better the role heterotrophic bacteria play in carbon cycling in seagrass estuaries. My dissertation research focuses on Florida Bay, a seagrass estuary that has experienced recent changes in carbon source availability, which may have altered ecosystem function. My dissertation research investigates the importance of seagrass, algal and/or cyanobacterial, and allochthonous-derived organic matter to heterotrophic bacteria in Florida Bay and helps establish the carbon base of the estuarine food web. ^ A three tiered approach to the study of heterotrophic bacterial carbon cycling and trophic influences in Florida Bay was used: (1) Spatiotemporal observations of environmental parameters (hydrology, nutrients, extracellular enzymes, and microbial abundance, biomass, and production); (2) Microbial grazing experiments under different levels of top-down and bottom-up influence; and (3) Bulk and compound-specific (bacteria-biomarker fatty acid analysis) stable carbon isotope analysis. ^ In Florida Bay, spatiotemporal patterns in microbial extracellular enzyme (also called ectoenzyme) activities indicate that microorganisms hydrolyzed selectively fractions of the estuarine organic matter pool. The microbial community hydrolyzed organic acids, peptides, and phosphate esters and did not use storage and structural carbohydrates. Organic matter use by heterotrophic bacterioplankton in Florida Bay was co-regulated by bottom-up (resource availability) and top-down (grazer mediated) processes. A bacterial carbon budget based on bacterial, epiphytic, and seagrass production indicates that heterotrophic bacterial carbon cycles are supported primarily through epiphytic production with mixing from seagrass production. Stable carbon isotope analysis of bacteria biomarkers and carbon sources in Florida Bay corroborate the results of the bacterial carbon budget. These results support previous studies of aquatic consumers in Florida Bay, indicating that epiphytic/benthic algal and/or cyanobacterial production with mixing from seagrass-derived organic matter is the carbon base of the seagrass estuarine food web. ^

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.

Geochemistry, fatty acid content and phylogenetic affiliation of soil samples from Livingston Island, South Shetland Archipelago, Antarctica

Microorganisms inhabit very different soil habitats in the ice-free areas of Antarctica, playing a major role in nutrient cycling in cold environments. We studied the soil characteristics and the dominant bacterial composition from nine different soil profiles located on Livingston Island (maritime Antarctica). The total carbon (TC) and total nitrogen (TN) values were high for the vegetated soils, decreasing with depth, whereas the values for the mineral soils were generally low. Soil pH was more acidic for moss-covered soils and neutral to alkaline for mineral soils. Numbers of culturable heterotrophic bacteria were higher at vegetated sites, but significant numbers were also detectable in carbon-depleted soils. Patterns of denaturing gradient gel electrophoresis (DGGE) revealed a highly heterogeneous picture throughout the soil profiles. Subsequent sequencing of DGGE bands revealed in total 252 sequences that could be assigned to 114 operational taxonomic units, showing the dominance of members of the Bacteroidetes and Acidobacteria. The results of phospholipid fatty acid analysis showed a lack of unsaturated fatty acids for most of the samples. Samples with a prevalence of unsaturated over saturated fatty acids were restricted to several surface samples. Statistical analysis showed that the dominant soil bacterial community composition is most affected by TC and TN contents and soil physical factors such as grain size and moisture, but not pH. Keywords

Microbial community composition and bacterioplankton at time series station Helgoland Roads, North Sea

A process of global importance in carbon cycling is the remineralization of algae biomass by heterotrophic bacteria, most notably during massive marine algae blooms. Such blooms can trigger secondary blooms of planktonic bacteria that consist of swift successions of distinct bacterial clades, most prominently members of the Flavobacteriia, Gammaproteobacteria and the alphaproteobacterial Roseobacter clade. This study explores such successions during spring phytoplankton blooms in the southern North Sea (German Bight) for four consecutive years. The surface water samples were taken at Helgoland Island about 40 km offshore in the southeastern North Sea in the German Bight at the station 'Kabeltonne' (54° 11.3' N, 7° 54.0' E) between the main island and the minor island, Düne (German for 'dune') using small research vessels (http://www.awi.de/en/expedition/ships/more-ships.html). Water depths at this site fluctuate from 6 to 10 m over the tidal cycle. Samples were processed as described previously (Teeling et al., 2012; doi:10.7554/eLife.11888.001) in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Assessment of absolute cell numbers and bacterioplankton community composition was carried out as described previously (Thiele et al., 2011; doi:10.1016/B978-0-444-53199-5.00056-7). To obtain total cell numbers, DNA of formaldehyde fixed cells filtered on 0.2 mm pore sized filters was stained with 4',6-diamidino-2-phenylindole (DAPI). Fluorescently labeled cells were subsequently counted on filter sections using an epifluores-cence microscope. Likewise, bacterioplankton community composition was assessed by catalyzedreporter deposition fluorescence in situ hybridization (CARD-FISH) of formaldehyde fixed cells on 0.2 mm pore sized filters.

(Table 4) Distribution of bacterial populations in sediments of ODP Hole 128-798B

Sediment whole-round cores from a dedicated hole (798B) were obtained for detailed microbiological analysis, down to 518 m below the seafloor (mbsf). These sediments have characteristic bacterial profiles in the top 6 mbsf, with high but rapidly decreasing bacterial populations (total and dividing bacteria, and concentrations of different types of viable heterotrophic bacteria) and potential bacterial activities. Rates of thymidine incorporation into bacterial DNA and anaerobic sulfate reduction are high in the surface sediments and decrease rapidly down to 3 mbsf. Methanogenesis from CO2/H2 peaks below the maximum in sulfate reduction and although it decreases markedly down the core, is present at low rates at all but one depth. Consistent with these activities is the removal of pore-water sulfate, methane gas production, and accumulation of reduced sulfide species. Rates of decrease in bacterial populations slow down below 6 mbsf, and there are some distinct increases in bacterial populations and activities that continue over considerable depth intervals. These include a large and significant increase in total heterotrophic bacteria below 375 mbsf, which corresponds to an increase in the total bacterial population, bacterial viability, a small increase in potential rates of sulfate reduction, and the presence of thermogenic methane and other gases. Bacterial distributions seem to be controlled by the availability of terminal electron acceptors (e.g., sulfate), the bioavailability of organic carbon (which may be related to the dark/light bands within the sediment), and biological and geothermal methane production. Significant bacterial populations are present even in the deepest samples (518 mbsf) and hence it seems likely that bacteria may continue to be present and active much deeper than the sediments studied here. These results confirm and extend our previous results of bacterial activity within deep sediments of the Peru Margin from Leg 112, and to our knowledge this is the first comprehensive report of the presence of active bacterial populations from the sediment surface to in excess of 500 mbsf and sediments > 4 m.y. old.

Utilização de diferentes fontes de carbono no cultivo do camarão litopenaeus vannamei em sistemas com bioflocos

A tecnologia do sistema de cultivo com bioflocos (BFT) permite a intensificação da densidade de estocagem, bem como o aumento da produtividade no qual exige esforços no manejo para a manutenção de qualidade de água. No entanto, um dos problemas é a liberação de nitrogênio através de alimento não consumidos, juntamente com as excretas dos organismos cultivados, principalmente na forma de amônia total. A adição de fontes de carbono orgânico é uma alternativa na redução de amônia tornando possível a conversão deste composto em proteína bacteriana, sendo disponível como alimento suplementar no ambiente de cultivo. Portanto foram testadas fontes de carbono como o melaço de cana-de-açúcar, dextrose e farelo de arroz no cultivo do camarão L. vannamei em sistemas BFT, avaliando a redução da concentração do nitrogênio amoniacal total em experimentos nas fases de berçário e engorda, bem como a análise de desempenho zootécnico dos animais. Os experimentos foram realizados utilizando caixas com volume útil de 800 L. O experimento berçário teve a duração de 35 dias, com densidade de estocagem de 1200 camarões m- ² e peso médio de 0,024±0,01 g. As fontes de carbono melaço de cana-de-açúcar (M) e farelo de arroz (F) foram combinadas em diferentes percentuais. No experimento engorda foi utilizada densidade de estocagem de 300 camarões m- ², peso médio de 4,09±0,51 g, durante 70 dias. Os tratamentos foram distinguidos pelas fontes de carbono dextrose e farelo de arroz. No experimento berçário a concentração da amônia foi significativamente menor (p<0,05) com o uso do melaço. O nitrito acumulou até o final do experimento, mas devido ao curto período experimental não interferiu nos índices de desempenho zootécnico, nos quais não apresentaram diferenças pelo uso das fontes de carbono. No experimento engorda, com o uso da dextrose, a concentração de amônia foi significativamente menor (p<0,05). Apesar de elevadas concentrações de nitrito, as sobrevivências foram similares e acima de 80%. Dados zootécnicos como peso final, ganho de peso semanal, conversão alimentar aparente e produtividade foram significativamente melhores (p<0,05) no tratamento farelo de arroz. Em ambos os experimentos as fontes de carbono de degradação rápida, como o melaço e a dextrose foram mais eficientes na redução de amônia. A degradação rápida destas fontes podem ter disponibilizado maiores teores de carbono como substrato para as bactérias heterotróficas metabolizarem a amônia, melhorando a qualidade da água.

Heterotrophic marine bacteria as supplementary feed for larval Penaeus monodon

The findings are presented of a study conducted to use autochthonously obtained, nonpathogenic heterotrophic marine bacteria as a substitute feed for microalgae in rearing larval Penaeus monodon. Eleven strains were isolated: Micrococcus (MCC), Staphylococcus, Streptococcus, Bacillus (two strains; BAC-1, BAC-2), Pseudomonas (two strains; PSM-1, PSM-2), Vibrio parahemolyticus, V. fluviatilis, Moraxella (MOR) and Flavobacterium. Six nonhemolytic strains were then chosen for the Penaeus monodon larval feed trials: BAC-1, BAC-2, PSM-1, PSM-2, MCC and MOR. The study demonstrates that bacterial biomass could be further investigated as a partial substitute for microalgae in penaeid shrimp larval rearing.