Diversity of methyl halide-degrading microorganisms in oceanic and coastal waters

Methyl halides have a significant impact on atmospheric chemistry, particularly in the degradation of stratospheric ozone. Bacteria are known to contribute to the degradation of methyl halides in the oceans and marine bacteria capable of using methyl bromide and methyl chloride as sole carbon and energy source have been isolated. A genetic marker for microbial degradation of methyl bromide ( cmuA ) was used to examine the distribution and diversity of these organisms in the marine environment. Three novel marine clades of cmuA were identified in unamended seawater and in marine enrichment cultures degrading methyl halides. Two of these cmuA clades are not represented in extant bacteria, demonstrating the utility of this molecular marker in identifying uncultivated marine methyl halide-degrading bacteria. The detection of populations of marine bacteria containing cmuA genes suggests that marine bacteria employing the CmuA enzyme contribute to methyl halide cycling in the ocean.     

Influence of UV-B radiation on bacterial activity in coastal waters

The impact of UV-B radiation (290–315 nm) on bacterialactivity and abundance in coastal water was studied in mesocosmexperiments in May 1994 and May 1995 at Kristineberg MarineResearch Station, Sweden. Mesocosms (6 m³) containing naturalpelagic communities were exposed either to ambient irradiation(AMB), ambient irradiation with enhanced UV-B (+UV) (0.7 W m^–24 h every day around noon), or ambient irradiation screenedfor UV-B (–UV). Bacterial activity in the mesocosms wasmeasured by means of thymidine incorporation in short-term testsduring incubations at ambient irradiation, at ambient irradiationwith enhanced UV-B, and at ambient irradiation screened forUV-B. In +UV mesocosms, bacterial activity was significantlystimulated when incubated at ambient radiation. The stimulatingeffect was suggested to be due to an increase in carbon or nutrientsupply through a photodegradation of recalcitrant dissolvedorganic material (DOM). Low attenuation coefficients for UV-Band PAR (400–700 nm) in the +UV mesocosms supported thishypothesis. The bacterial activity in +UV mesocosms, however,was inhibited when incubations were made at enhanced UV-B irradiation,implying that the bacteria had become more sensitive to UV-Bradiation. The increased sensitivity to UV-B exposure in bacterialassemblages that already had been exposed and stressed by UV-Bradiation is suggested to be due to an overburdening of theenergy-consuming DNA repair mechanism. The data suggest thatincreased UV-B radiation, which might occur with ozone depletion,may both stimulate and suppress bacterial activity in coastalwaters, implying that the net outcome of enhanced UV-B radiationcould be an unchanged bacterial activity.     

Nitrogen metabolism by heterotrophic bacterial assemblages in Antarctic coastal waters

Field studies to examine the in situ assimilation and production of ammonium (NH₄ ⁺) by bacterial assemblages were conducted in the northern Gerlache Strait region of the Antarctic Peninsula. Short term incubations of surface waters containing ¹⁵N-NH₄ ⁺ as a tracer showed the bacterial population taking up 0.041–0.128 g-atoms Nl^–1d^–1, which was 8–25% of total NH₄ ⁺ uptake rates. The large bacterial uptake of NH₄ ⁺ occurred even at low bacterial abundance during a rich phytoplankton bloom. Estimates of bacterial production using ³H-leucine and -adenine were l.0gCl^–1 d^–1 before the bloom and 16.2 g Cl^–1 d^–1 at the bloom peak. After converting bacterial carbon production to an estimate of nitrogen demand, NH₄ ⁺ was found to supply 35–60% of bacterial nitrogen requirements. Bacterial nitrogen demand was also supported by dissolved organic nitrogen, generally in the form of amino acids. It was estimated, however, that 20–50% of the total amino acids taken up were mineralized to NH₄ ⁺. Bacterial production of NH₄ ⁺ was occurring simultaneously to its uptake and contributed 27–55% of total regenerated NH₄ ⁺ in surface waters. Using a variety of ¹⁵N-labelled amino acids it was found that the bacteria metabolized each amino acid differently. With their large mineralization of amino acids and their relatively low sinking rates, bacteria appear to be responsible for a large portion of organic matter recycling in the upper surface waters of the coastal Antarctic ecosystem.     

Mixotrophic haptophytes are key bacterial grazers in oligotrophic coastal waters

Grazing rate estimates indicate that approximately half of the bacterivory in oligotrophic oceans is due to mixotrophic flagellates (MFs). However, most estimations have considered algae as a single group. Here we aimed at opening the black-box of the phytoflagellates (PFs) <20 μm. Haptophytes, chlorophytes, cryptophytes and pigmented dinoflagellates were identified using fluorescent in situ hybridization or by standard 4′,6-diamidino-2-phenylindole staining. Their fluctuations in abundance, cell size, biomass and bacterivory rates were measured through an annual cycle in an oligotrophic coastal system. On average, we were able to assign to these groups: 37% of the total pico-PFs and 65% of the nano-PFs composition. Chlorophytes were mostly picoplanktonic and they never ingested fluorescently labeled bacteria. About 50% of the PF <20 μm biomass was represented by mixotrophic algae. Pigmented dinoflagellates were the least abundant group with little impact on bacterioplankton. Cryptophytes were quantitatively important during the coldest periods and explained about 4% of total bacterivory. Haptophytes were the most important mixotrophic group: (i) they were mostly represented by cells 3–5 μm in size present year-round; (ii) cell-specific grazing rates were comparable to those of other bacterivorous non-photosynthetic organisms, regardless of the in situ nutrient availability conditions; (iii) these organisms could acquire a significant portion of their carbon by ingesting bacteria; and (iv) haptophytes explained on average 40% of the bacterivory exerted by MFs and were responsible for 9–27% of total bacterivory at this site. Our results, when considered alongside the widespread distribution of haptophytes in the ocean, indicate that they have a key role as bacterivores in marine ecosystems.     

Contrasting effects of substrate and grazer manipulations on picoplankton in oceanic and coastal waters off Brazil

In two contrasting regions off the coast of Brazil, picoplankton(<1 µm) responses to removal of larger grazers andto the additions of glucose and amino acids were determined.Effects of glucose and amino acid additions (1 µM) onparticulate nitrogen and chlorophyll a concentrations, and onrates of NH₄⁺ uptake and regeneration, were observed after 5h pre-incubation. In the oceanic waters, removal of the >1µm fraction had no significant effect on the chlorophylla of the picoplankton after 5 h. However, the addition of glucosestimulated both uptake and regeneration by a mean of 27%, andthe addition of arginine led to significant decreases in therates of NH₄⁺ uptake and regeneration. In contrast, in the coastalwaters, significant increases in chlorophyll and particulatenitrogen concentrations were found after 5 h incubation in boththe amended samples and in the controls, and mean rates of NH₄⁺uptake and regeneration were affected to a lesser degree bythe additions of either glucose or amino acids than in the oceanicwaters. The oceanic responses were suggestive of carbon limitationof heterotrophic bacteria. In the coastal region, on the otherhand, the supply of organic carbon and nitrogen was likely tohave been sufficient to meet the nutritional requirements ofthe heterotrophic bacteria and cyanobacteria. Grazing by largerorganisms on the picoplankton appeared to play a more significantrole in the nitrogen cycle in the coastal waters than in theoceanic waters.     

A new genus and two new species of marine free-living nematodes from the coastal waters of Southern Vietnam

A new genus and two new species of free-living marine nematodes from sediments in the coastal zone of the South China Sea (Vietnam) are described. Cyartonemoides gen. n. morphologically resembles Cyartonema Cobb, 1920, but differs from it in having a well-developed cephalic capsule. Cyartonemoides foetidus gen. n., sp. n. is the type and the only species of the genus. Campylaimus abnormis sp. n. differs from all species of the genus Campylaimus Cobb, 1920 by the shape of the amphidial fovea and shorter lateral fields.     

Three new species of nematodes (Nematoda: Enoplida) from coastal waters of Vietnam

Three new species of free-living nematodes of the order Enoplida from coastal shallow waters of northern Vietnam are described and illustrated. Paramesacanthion vietnamicum sp. n. is morphologically close to P. oxycephalum (Ditlevsen, 1926), P. truncum Vitiello, 1971, and P. hirsutum Warwick, 1970; however, it differs in lacking subcephalic setae and in having articulate cephalic setae in the males. Viscosia pygmaea sp. n. is morphologically similar to V. parva Kreis, 1929 but differs in having a shorter body and a shorter and thicker tail in the females. V. pygmaea is distinguished from V. megalaima (Ditlevsen, 1928) by its shorter body, longer cephalic setae, more slender tail, and the position of the vulva. Viscosia longicaudatoides sp. n. can be distinguished from V. parva and V. timmi Gagarin, Nguyen Vu Thanh, 2007 by its thinner body, longer and more slender tail, and shorter and narrower stoma. In contrast to V. timmi, it has short spicules and lacks vesicle-like cells between the gut and the longitudinal chords.     

Potential phytoplankton indicator species for monitoring Baltic coastal waters in the summer period

There are very few time series documenting clear trends of change in the biomass of total phytoplankton or single taxa that coincide with trends of increasing nutrient concentrations. Weekly or biweekly monitoring since 1997 on a cross section of the central Gulf of Finland (NE Baltic Sea) with similar climatic and hydrographic conditions, but different nutrient levels, provided a uniform dataset. In order to evaluate seasonal (June–September) patterns of phytoplankton succession, more than 1,200 samples were statistically analyzed by selecting 12 dominant taxa using wet weight biomass values. In addition, the continuously measured hydrographic parameters on board the ships of opportunity, and simultaneous nutrient analyses gave high frequency information on the water masses. The objective of this study was to identify the taxa that may prove indicative in the assessment of eutrophication in the appropriate monitoring time periods. None of the most common bloom-forming species (Aphanizomenon sp., Nodularia spumigena, and Heterocapsa triquetra) showed reliable correlations with enhanced nutrient concentrations. The species we suggest as reliable eutrophication indicators—oscillatorialean cyanobacteria and the diatoms Cyclotella choctawhatcheeana and Cylindrotheca closterium—showed the best relationships with total phosphorus concentrations. Their maxima appear toward the end of July or in August–September when phytoplankton community structure is more stable, and less frequent observations may give adequate results. Another diatom, Skeletonema costatum, exhibited stronger correlations with dissolved inorganic and total nitrogen in June, during the period of the summer phytoplankton minimum. Guest editors: J. H. Andersen & D. J. Conley Eutrophication in Coastal Ecosystems: Selected papers from the Second International Symposium on Research and Management of Eutrophication in Coastal Ecosystems, 20–23 June 2006, Nyborg, Denmark     

A harpacticoid copepod Microsetella spp. from sub-Arctic coastal waters and its sensitivity towards the polyaromatic hydrocarbon pyrene

Species of the harpacticoid copepod genus Microsetella are commonly reported to occur in Arctic and sub-Arctic coastal waters, but nothing has yet been reported on their sensitivity towards toxic substances. Effects of the polyaromatic hydrocarbon pyrene on Microsetella spp. from Western Greenland were investigated by looking at survival of females, feeding status, and nucleic acid content after a 96-h exposure. Less than 10% survived at 100 nM exposure concentration, and a 50% reduced survival was also evident at 0.1 and 10 nM. The RNA:DNA ratio was significantly higher, 2.1 ng/individual, at the lowest concentration of 0.01 nM compared to 0.9 ng/individual in the control, which indicates increased metabolic activities. A reduced DNA content in higher exposure concentrations of 1–100 nM suggests inhibition of egg development. Gut content was significantly declining with increasing exposure concentrations with only 2% of exposed females displaying full guts at 100 nM pyrene. Together with reduced feeding activity, effects at the population level can be anticipated, but would have to be confirmed in future experiments. The data suggests a higher sensitivity of Microsetella spp. compared to other Arctic copepods, which implies more severe effects from oil on the pelagic food web in the areas and periods where Microsetella spp. dominates Arctic plankton food webs.     

Habitat partitioning by whiting species (Sillaginidae) in coastal waters

Synopsis The ways in which the distributions of six species of whiting (Sillaginidae) in the coastal marine waters of south-western Australia are related to the type of substrate (bare sand vs. seagrass), degree of exposure of habitat, water depth and body size have been investigated. Whiting in near shore waters (< 1.5 m) were sampled using a fine-meshed seine net, while those in shallow (5–15 m) and deep (20–35 m) waters of the inner continental shelf were sampled with a trawl net. Shallow nearshore waters are shown to provide nursery habitats for five of the six whiting species. In these waters, Sillaginodes punctata, Sillago burrus, Sillago schomburgkii and Sillago vittata mainly occur in protected areas, while Sillago bassensis predominantly occupies areas that are more exposed to wave and swell activity. The first three of these species also use estuaries as nursery areas. In nearshore waters, whiting were captured almost exclusively over bare sand, rather than in interpersed beds of the seagrass Posidonia spp., presumably reflecting the fact that the dense canopies produced by the wide blades of Posidonia spp. must inhibit penetration by the benthic whiting species. As 0 + S. punctata increase in size, they tend to move offshore during the day and inshore at night. Many mature representatives of S. schomburgkii are present in nearshore areas, whereas the other four species move offshore into inner-shelf waters as they increase in length. Sillago burrus and S. vittata remain in shallow inner-shelf waters, whereas the larger S. bassensis subsequently migrate into deeper inner-shelf waters. Large Sillago bassensis thus co-occurs with Sillago robusta, which is mainly found in those deeper waters, but does not reach as large a size. The larger S. punctata occupy areas near reefs which could not be sampled by trawl netting. There are thus interspecific differences in (i) the times of recruitment of the 0 + age class into nearshore areas, (ii) the types of habitat occupied during juvenile and adult life, and (iii) the degree to which fish move into more offshore waters as they increase in length, and one species is restricted to deeper waters. The resultant partial segregation among habitats of the coastal waters of south-western Australia by different size groups of these relatively abundant whiting species presumably reduces the potential for intra- and interspecific competition amongst these species.     

Kinetic modulation of bacterial hydrolases by microbial community structure in coastal waters

In this study, we hypothesized that shifts in the kinetic parameters of extracellular hydrolytic enzymes may occur as a consequence of seasonal environmental disturbances and would reflect the level of adaptation of the bacterial community to the organic matter of the ecosystem. We measured the activities of enzymes that play a key role in the bacterial growth (leucine aminopeptidase, β- and α-glucosidases) in surface coastal waters of the Eastern Cantabrian Sea and determined their kinetic parameters by computing kinetic models of distinct complexity. Our results revealed the existence of two clearly distinct enzymatic systems operating at different substrate concentrations: a high-affinity system prevailing at low substrate concentrations and a low-affinity system characteristic of high substrate concentrations. These findings could be the result of distinct functional bacterial assemblages growing concurrently under sharp gradients of high-molecular-weight compounds. We constructed an ecological network based on contemporaneous and time-delayed correlations to explore the associations between the kinetic parameters and the environmental variables. The analysis revealed that the recurring phytoplankton blooms registered throughout the seasonal cycle trigger the wax and wane of those members of the bacterial community able to synthesize and secrete specific enzymes.     

Degradation of different hydrocarbons and production of biosurfactant byPseudomonas aeruginosa isolated from coastal waters

Summary A bacterium isolated from an oil spillage sample and identified asPseudomonas aeruginosa degraded hexadecane and heptadecane by 47% and 58% with 9% and 12% of total carbon from the respective substrates being liberated as CO₂. With octadecane and nonadecane as substrates, 73% and 60% were biodegraded while 27% and 25% of total carbon was evolved as CO², respectively. Production of biosurfactant by this bacterium was studied using hexadecane 5% (v/v) as substrate. The surface tension of spent culture medium, as well as the supernatant, was 30 mN/m compared to 71 mN/m for water. When the supernatant was mixed with hexadecane (15, v/v) a stable emulsion was formed which deteriorated only by 10% after one month.

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Dégradation de différents hydrocarbures et production de biosurfactants parPseudomonas aeruginosa isolé d'eaux côtières

Résumé Une bactérie, isolée d'un échantillon d'hydrocarbures épandus, et identifiée commePseudomonas aeruginosa, dégrade l'hexaet l'heptadécane à raison respective de 47 et de 58% du carbone total avec 9 et 12% des substrats respectifs libérés sous la forme de CO₂. Avec l'octa- et le nonadécane comme substrats, la biodégradation atteint respectivement 73 et 60% avec 27 et 25% du carbone total transformé en CO₂. On a étudié la production de biosurfactant par cette bactérie en utilisant l'hexadécane à 5% (v/v) comme substrat. La tension superficielle de la liqueur mixte, comme celle de son surnageant atteint 30 mN/m par comparaison à 71 mN/m pour l'eau. Lorsque le surnageant est mélangé à l'hexadécane (15, v/v), on forme une émulsion stable qui ne se détériore que de 10% au bout d'un mois.

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This work was carried out at the Biotechnology Laboratories of the Nuclear Institute for Agriculture & Biology (NIAB), Faisalabad.     

Ecohydrology as a new tool for sustainable management of estuaries and coastal waters

Throughout the world, estuaries and coastal waters have experienced degradation. Present proposed remedial measures based on engineering and technological fix are not likely to restore the ecological processes of a healthy, robust estuary and, as such, will not reinstate the full beneficial functions of the estuary ecosystem. The successful management of estuaries and coastal waters requires an ecohydrologybased, basin-wide approach. This necessitates changing present practices by official institutions based on municipalities or counties as an administrative unit, or the narrowly focused approaches of managers of specific activities (e.g., farming and fisheries, water resources, urban and economic developments, wetlands management and nature conservationists). Without this change in thinking and management concept, estuaries and coastal waters will continue to degrade, whatever integrated coastal management plans are implemented. To help in this process of change there is a need to (1) develop a profound understanding of the effects of biota and biotic processes on mediating estuary response to changing hydrology, sediment and nutrient flux and of the biota on hydrology at the river basin scale, and (2) to develop science-based remediation measures at the river basin scale, with elements of ecohydrology and phytotechnology at their core, to strengthen the ability of the biota to sustain and adapt to human-induced stresses.This revised version wa published online in March 2005 with corrections to the issue cover date.     

Recurrent seasonal changes in bacterial growth efficiency,metabolism and community composition in coastal waters

The microbial response to environmental changes in coastal waters of the eastern Cantabrian Sea was explored for four years by analysing a broad set of environmental variables along with bacterial community metabolism and composition. A recurrent seasonal cycle emerged, consisting of two stable periods, characterized by low bacterial metabolic activity (winter) from October to March, and high bacterial metabolic activity (summer) from May to August. These two contrasting periods were linked by short transition periods in April (T_A) and September (T_S). The phylogenetic groups Alphaproteobacteria and Bacteroidetes were dominant during winter and summer respectively, and their recurrent alternation was mainly driven by the bloom of eukaryotic phytoplankton before T_A and the bloom of prokaryotic phytoplankton before T_S. Bacterial growth efficiency remained high and stable during the winter and summer periods but dropped during the two short transition periods. Our results suggest that bacterial growth efficiency should be considered a very resilient property that reflects different stages in the adaptation of the bacterial community composition to the environmental changes occurring throughout the seasonal cycle in this coastal ecosystem.     

我国沿海棱鳀属鱼类的物种鉴定与系统发育

利用DNA条形码技术对中国沿海分布的6种棱鳀属(Thryssa)鱼类样品进行了物种鉴定, 并每种取5尾用于探讨该属系统发育关系。结果显示: 棱鳀属鱼类的主要形态鉴别特征为上颌骨伸达位置和第一鳃耙的下鳃耙数量。在525 bp的目的片段上有175个变异位点, 其中简约信息位点172个, 单一信息位点3个, 无插入缺失现象, 转换数为182, 颠换数为57。A+T含量明显高于G+C含量, 并且表现出明显的反G偏倚。结合GenBank中相关的同源序列进行比较发现, 所有序列明显分为10个组群, 表明已提交的棱鳀属鱼类COI基因序列中仍存在一定的问题。从各组群间的遗传距离和氨基酸遗传差异水平可以看出, 10个组群应为不同的有效种, 但是否存在隐存种还有待于进一步确定。从NJ树上可以看出, 长颌棱鳀(T. setirostris)是最先分化出的物种, 保持着最原始的特征, 而中颌棱鳀(T. mystax)与黄吻棱鳀(T. vitrirostris)聚类到一起, 二者间存在共享单倍型。棱鳀属鱼类最早分化于中新世早期。在今后的研究中仍需要结合更多的分子标记对中颌棱鳀和黄吻棱鳀的分类地位作进一步的探讨。     

Grazing impact of copepod assemblages and gravitational flux in coastal and oceanic waters off central Chile during two contrasting seasons

In evaluating carbon flux in coastal and oceanic waters offcentral Chile (~36°S), the grazing pressure by copepod size-assemblagesand the gravitational flux from the surface layer were estimatedduring two contrasting seasons: spring upwelling (October 1998)and winter (July 1999) periods. Grazing pressure upon phytoplanktonbiomass was small (<5%) during both periods at all stations.It was, however, an important proportion of primary productionat the coast during the spring (17–43%) but minimal inwinter (<5%) while, at the oceanic station, it was significantduring both seasons (13–46%). Similarly, the downwardflux of particulate organic carbon was a significant percentageof primary production at the coast during the spring (31%) andless so in winter (15%); at the oceanic station, it was a higherfraction during both seasons (46–47%). Copepod pelletswere only a minor component of the faecal flux, suggesting thatthey were rapidly recycled in the water column. The seasonaldifferences in these carbon fluxes in the coastal upwellingzone were related directly to the larger quantities of organicmatter in the water column during the spring upwelling period,including higher chlorophyll a concentrations and primary productionrates. During the winter, the particulate organic carbon appearsto be mainly recycled in the water column. In the oceanic zone,in contrast to what is expected, a large percentage of the primaryproduction appears to be exported during both periods, thoughconsumption by copepod assemblages was also important, suggestingsignificant horizontal carbon export from the coast to the openocean.