A metagenomic assessment of winter and summer bacterioplankton from Antarctica Peninsula coastal surface waters

Antarctic surface oceans are well-studied during summer when irradiance levels are high, sea ice is melting and primary productivity is at a maximum. Coincident with this timing, the bacterioplankton respond with significant increases in secondary productivity. Little is known about bacterioplankton in winter when darkness and sea-ice cover inhibit photoautotrophic primary production. We report here an environmental genomic and small subunit ribosomal RNA (SSU rRNA) analysis of winter and summer Antarctic Peninsula coastal seawater bacterioplankton. Intense inter-seasonal differences were reflected through shifts in community composition and functional capacities encoded in winter and summer environmental genomes with significantly higher phylogenetic and functional diversity in winter. In general, inferred metabolisms of summer bacterioplankton were characterized by chemoheterotrophy, photoheterotrophy and aerobic anoxygenic photosynthesis while the winter community included the capacity for bacterial and archaeal chemolithoautotrophy. Chemolithoautotrophic pathways were dominant in winter and were similar to those recently reported in global ‘dark ocean'' mesopelagic waters. If chemolithoautotrophy is widespread in the Southern Ocean in winter, this process may be a previously unaccounted carbon sink and may help account for the unexplained anomalies in surface inorganic nitrogen content.     

Pronounced summer to winter differences and higher wintertime richness in coastal Antarctic marine bacterioplankton

Marine bacterioplankton studies over the annual cycle in polar systems are limited due to logistic constraints in site access and support. Here, we conducted a comparative study of marine bacterioplankton sampled at several time points over the annual cycle (12 occasions each) at sub-Antarctic Kerguelen Islands (KI) and Antarctic Peninsula (AP) coastal sites in order to establish a better understanding of the extent and nature of variation in diversity and community structure at these different latitudes (49-64S). Molecular methods targeting the 16S rRNA gene (DGGE, CE-SSCP and tag pyrosequencing) suggest a strong seasonal pattern with higher richness in winter and a clear influence of phytoplankton bloom events on bacterioplankton community structure and diversity in both locations. The distribution of sequence tags within Gammaproteobacteria, Alphaproteobacteria and Bacteriodetes differed between the two regions. At both sites, several abundant Rhodobacteraceae, uncultivated Gammaproteobacteria and Bacteriodetes-associated tags displayed intense seasonal variation often with similar trends at both sites. This enhanced understanding of variability in dominant groups of bacterioplankton over the annual cycle contributes to an expanding baseline to understand climate change impacts in the coastal zone of polar oceans and provides a foundation for comparison with open ocean polar systems.     

Relationships between bacterioplankton, chl a and temperature in Antarctic surface waters in summer

Spatial variations of bacterio- and phytoplankton were studied in order to compare their relationship in open-sea and coastal areas. Sampling was done quasi-synoptically south of the Antarctic Convergence in the Lazarev Sea and in the eastern part of the Weddell Sea during austral mid-summer. Thymidine incorporation rate was on average 1.10 nmol/m³ per hour in the open sea and 4.04  nmol/m³ per hour in the coastal area, bacterial abundance was 4.44 × 10¹¹ and 6.11 × 10¹¹ cells/m³ and chlorophyll a (chl a) was 0.43 and 2.42 mg/m³, respectively. Thymidine incorporation rate and chl a correlated positively in both the open-sea and coastal samples. In the coastal area bacterial numbers also correlated positively with chl a. The scale of spatial resolution was not important for detecting empirical relationships between phytoplankton and bacterioplankton parameters. In the coastal area, the low bacterial biomass in relation to chl a concentration compared to other oceans, indicates that generalised relationships between these parameters are not valid in Antarctic coastal waters. Grazing could not explain the discrepancy. The results suggest a strong coupling between phytoplankton and bacterioplankton. In addition, the results suggest that the bacterial assemblage in the coastal area was psychrophilic and well adapted to the prevailing low temperatures. Received: 18 October 1996 / Accepted: 8 December 1996     

Seasonal patterns in the sunlight sensitivity of bacterioplankton from Mediterranean surface coastal waters

The sensitivity of coastal marine bacterioplankton to natural photosynthetically active radiation (PAR, 400-700?nm) and ultraviolet radiation (UVR, 280-400?nm) was evaluated in five experiments over a seasonal cycle in the Blanes Bay, NW Mediterranean Sea. Exposure to natural solar radiation generally inhibited bulk bacterial activities or damaged membrane integrity when irradiances were high (i.e. spring and summer experiments) and, in general, UVB (280-320?nm) accounted for most of the inhibition. When assessing activity ((3) H-leucine uptake) at the single-cell level by microautoradiography and rRNA gene probing, seasonally varying responses and sensitivities were found among bacterial groups. While autumn and winter irradiances seemed too low to cause changes in activity, variable effects were found in spring and summer. SAR11 was consistently inhibited by UVR and PAR exposure, whereas Gammaproteobacteria and Bacteroidetes showed higher resistance. Roseobacter, Synechococcus and the NOR5 clade were occasionally photostimulated in their activity, mainly because of PAR. Our results indicate that a component of seasonality exists in the bacterial responses to solar radiation, which vary not only depending on the irradiance and the spectral characteristics, but also on the previous light history and the taxonomic composition of the community.     

Incorporation of glucose under anoxic conditions by bacterioplankton from coastal North Sea surface waters

It has been hypothesized that the potential for anaerobic metabolism might be a common feature of bacteria in coastal marine waters (L. Riemann and F. Azam, Appl. Environ. Microbiol. 68: 5554-5562, 2002). Therefore, we investigated whether different phylogenetic groups of heterotrophic picoplankton from the coastal North Sea were able to take up a simple carbon source under anoxic conditions. Oxic and anoxic incubations (4 h) or enrichments (24 h) of seawater with radiolabeled glucose were performed in July and August 2003. Bacteria with incorporated substrate were identified by using a novel protocol in which we combined fluorescence in situ hybridization and microautoradiography of cells on membrane filters. Incorporation of glucose under oxic and anoxic conditions was found in alpha-Proteobacteria, gamma-Proteobacteria, and the Cytophaga-Flavobacterium cluster of the Bacteroidetes at both times, but not in marine Euryarchaeota. In July, the majority of cells belonging to the alpha-proteobacterial Roseobacter clade showed tracer incorporation both in oxic incubations and in oxic and anoxic enrichments. In August, only a minority of the Roseobacter cells, but most bacteria affiliated with Vibrio spp., were able to incorporate the tracer under either condition. A preference for glucose uptake under anoxic conditions was observed for bacteria related to Alteromonas and the Pseudoalteromonas-Colwellia group. These genera are commonly considered to be strictly aerobic, but facultatively fermentative strains have been described. Our findings suggest that the ability to incorporate substrates anaerobically is widespread in pelagic marine bacteria belonging to different phylogenetic groups. Such bacteria may be abundant in fully aerated coastal marine surface waters.     

雷州半岛近海夏季浮游植物和浮游细菌生物量的分布及其影响因素

于2010年7月(夏季)调查了雷州半岛近海海域浮游植物和细菌生物量的空间分布特征,并分析了其与海区主要环境因子间的相互关系。结果表明:雷州半岛近海海域夏季浮游植物生物量的变化范围为15.66～1114.92mg.m-3;平均值为192.49mg.m-3;夏季浮游细菌生物量的变化范围为3.36～50.12mgC.m-3,平均值为18.43mgC.m-3;浮游植物生物量水平分布格局在不同区域间没有显著差异,浮游细菌生物量的水平分布呈现西部海区>东部海区>南部海区的格局,差异极显著;浮游植物和浮游细菌生物量在表底层的垂直分布格局没有明显的规律,表、底层生物量或高或低,差异不显著;浮游植物和浮游细菌生物量多体现近岸站位>中间站位>远岸站位,即从陆向向海向呈递减的分布格局;夏季雷州半岛近海海域浮游细菌生物量与水温、pH和硅酸盐呈显著或极显著正相关,与盐度、TOC和磷酸盐呈极显著负相关;浮游植物生物量与pH和DO呈显著或极显著正相关,与盐度和TOC呈显极显著负相关;浮游植物生物量与浮游细菌生物量存在显著的正相关性,二者存在着相互影响的调控关系。     

深圳近海表层浮游细菌分布特征及其环境影响因素

于2015年3月、5月、8月和10月在深圳市近岸海域(珠江口、深圳湾和大亚湾)采集表层水样,利用流式细胞仪测定总浮游细菌、高DNA含量亚群细菌(HNA)、低DNA含量亚群细菌(LNA)的丰度,分析它们的时空分布特点,阐释环境因子对浮游细菌时空分布格局的影响。结果表明,珠江口、深圳湾和大亚湾海域表层浮游细菌的平均丰度依次降低,分别为3.82×10~6个/mL、7.67×10~6个/mL和3.38×10~6个/mL。珠江口海域浮游细菌丰度由远岸到近岸递增,深圳湾海域湾内各站位浮游细菌丰度差异较小,大亚湾海域浮游细菌丰度空间差异不显著(P0.05)。浮游细菌丰度时间差异主要受温度影响,空间差异主要受营养盐和叶绿素a影响。HNA亚群丰度时空差异性比LNA亚群的大,HNA亚群受温度影响显著(P0.01),而LNA亚群与温度相关性不显著(P0.05)。环境对HNA和LNA亚群丰度的影响有许多相似之处,但两者对某些环境因子有着不同的响应,说明它们在近海表层生态系统中可能扮演着部分重叠但略有不同的角色。     

冬夏季雷州半岛附近海域微微型光合浮游生物的类群变化及环境影响

2006年夏季和冬季对雷州半岛附近海域微微型光合浮游生物的类群数量与分布进行分析研究.结果表明:该海区微微型光合浮游生物的主要类群为聚球藻(Synechococcus)和微微型真核生物(pico-eukaryotes),二者在夏季的数量变化分别为(5.74±5.0)×104cell/ml和(2.33±1.82)×103cell/ml,冬季分别为(1.57±2.17)×103cell/ml和(4.17±4.40)×103cell/ml.聚球藻的丰度夏季高于冬季,高值区位于雷州湾海区;而微微型光合真核生物的丰度冬季高于夏季,冬季高值出现在雷州湾内D7站表层.雷州半岛西部海区微微型光合浮游生物的丰度夏、冬季变化比雷州湾附近海区明显,营养盐、温度、潮汐等是制约其数量变化的主要因子.     

Feeding and diel vertical migration cycles of Metridia gerlachei (Giesbrecht) in coastal waters of the Antarctic Peninsula

Diel vertical migration and feeding cycles of adult female Metridia gerlachei in the upper 290 m of a 335-m water column were measured during a total of 65 h in two periods of early summer (Dec 20–21 and Dec 25–26, 1991). Samples collected in eight depth strata by 35 MOCNESS tows (333-m mesh) were analyzed for abundance and mean individual gut pigment content. Most of the copepod population was concentrated in a 50-m depth interval at all times. Feeding began simultaneously with nocturnal ascent from a depth of 200–250 m at 18:00 h (local time), when the relative change in ambient light intensity was greatest. Ingestion rate increased exponentially (k_i = 0.988 h^–1) at double the gut evacuation rate (k_e = 0.488 h^–1) as the population moved upward at 22.3–26.5 m h^–1 through increasing concentrations of particulate chlorophyll-a. Although the bulk of the population did not move to depths shallower than 50 m, and began its downward migration at a rate of 20.8–31.7 mh^–1 in complete darkness, individual females continued to make brief excursions into chlorophyll-rich surface waters (4–8 g l^–1) during the first few hours of population descent. Ingestion rate diminished abruptly by one order of magnitude (k_i = 0.068 h^–1) at dawn ( 0330 h). Within four more hours, the population had reached its daytime depth and gut pigment content remained constant at a minimum value until the next migration cycle. No feeding appeared to take place at depth during the day. Ingestion by M. gerlachei females removed < 4% of daily primary production, with only 20% of this amount being removed from surface waters by active vertical transport.     

Light enhanced amino acid uptake by dominant bacterioplankton groups in surface waters of the Atlantic Ocean

(35)S-Methionine and (3)H-leucine bioassay tracer experiments were conducted on two meridional transatlantic cruises to assess whether dominant planktonic microorganisms use visible sunlight to enhance uptake of these organic molecules at ambient concentrations. The two numerically dominant groups of oceanic bacterioplankton were Prochlorococcus cyanobacteria and bacteria with low nucleic acid (LNA) content, comprising 60% SAR11-related cells. The results of flow cytometric sorting of labelled bacterioplankton cells showed that when incubated in the light, Prochlorococcus and LNA bacteria increased their uptake of amino acids on average by 50% and 23%, respectively, compared with those incubated in the dark. Amino acid uptake of Synechococcus cyanobacteria was also enhanced by visible light, but bacteria with high nucleic acid content showed no light stimulation. Additionally, differential uptake of the two amino acids by the Prochlorococcus and LNA cells was observed. The populations of these two types of cells on average completely accounted for the determined 22% light enhancement of amino acid uptake by the total bacterioplankton community, suggesting a plausible way of harnessing light energy for selectively transporting scarce nutrients that could explain the numerical dominance of these groups in situ.     

夏季南黄海冷水团及其周边海域小型底栖动物类群组成与分布

对2011年6月南黄海冷水团及其周边海域23个站位的小型底栖动物类群组成、丰度、生物量和空间分布及其与环境因子的关系进行了研究。结果表明,调查海域共鉴定出小型底栖动物20个类群,平均丰度为(1194±873)个/10 cm~2,平均生物量为(881±669)μg干重/10 cm~2,其中自由生活海洋线虫是绝对优势类群,占小型底栖动物总丰度的89.7%,其次为底栖桡足类(5.5%)、甲壳类幼体(1.8%)、多毛类(1.2%);对生物量的贡献上依次为海洋线虫(49.0%)、多毛类(22.9%)、桡足类(13.9%)、介形类(7.8%)、涡虫(2.0%)。在垂直分布上,79.1%的小型底栖动物分布在沉积物0—2 cm的表层,16.4%分布在2—5 cm的次表层,4.5%的小型底栖动物分布在5—8 cm的下层。与环境因子的相关性分析表明,小型底栖动物的总丰度和总生物量与沉积物叶绿素a含量显著正相关;小型底栖动物的生物量和沉积物中部分重金属(Pb、Cu、Fe、Ni、Co)含量呈显著负相关,但与Cd含量呈极显著正相关。BIOENV分析结果表明,沉积物含水量、有机质含量和分选系数组合最能解释小型底栖动物类群组成分布差异。根据小型底栖动物的类群组成可将研究海域划分为3个区域,包括:冷水团中央区域,冷水团边缘区和近岸区,其中冷水团边缘区丰度和生物量最高,冷水团区域次之,近岸区最低;整个冷水团海域小型底栖动物丰度和生物量分别是非冷水团海域的2.3倍和2.1倍。     

海洋石油污染物的微生物降解与生物修复

石油是海洋环境的主要污染物 ,已经对海洋及近岸环境造成了严重的危害。微生物降解是海洋石油污染去除的主要途径。海洋石油污染物的微生物降解受石油组分与理化性质、环境条件以及微生物群落组成等多方面因素的制约 ,N和P营养的缺乏是海洋石油污染物生物降解的主要限制因子。在生物降解研究基础上发展起来的生物修复技术在海洋石油污染治理中发展潜力巨大 ,并且取得了一系列成果。介绍了海洋中石油污染物的来源、转化过程、降解机理、影响生物降解因素及生物修复技术等方面内容 ,强调了生物修复技术在治理海洋石油污染环境中的优势和重要性 ,指出目前生物修复技术存在的问题。     

Seasonality in bacterial diversity in north-west Mediterranean coastal waters: assessment through clone libraries, fingerprinting and FISH

We combined denaturing gradient gel electrophoresis (DGGE), catalysed reporter deposition-FISH (CARD-FISH) and clone libraries to investigate the seasonality of the bacterial assemblage composition in north-west Mediterranean coastal waters. DGGE analysis indicated that bacterial diversity changed gradually throughout the year, although with a clear distinction of the summer period. Alphaproteobacteria were the dominant group on an annual basis [29% of the DAPI (4',6-diamidino-2-phenylindole) counts by CARD-FISH, and 70% of the bacterial clones]. The SAR11 clade was most abundant during spring and summer (>20% of DAPI counts), while the Roseobacter clade was abundant primarily in winter and spring (up to 7% of DAPI counts). The phylum Bacteroidetes constituted the second most important group and was quantitatively uniform throughout the year (average 11% of the DAPI counts). Gammaproteobacteria showed a peak during summer (8% of DAPI counts), when most of them belonged to the NOR5 cluster. Clone libraries and CARD-FISH showed reasonable agreement in the quantitative proportions of Bacteroidetes and Gammaproteobacteria, but Alphaproteobacteria were overrepresented in clone libraries. Sequencing of the most predominant DGGE bands failed to detect the SAR11 group despite their high abundance. The combination of the three molecular approaches allowed a comprehensive assessment of seasonal changes in bacterial diversity.     

Effects of surface fouling organisms on the occurrence of fungi on submerged pine blocks in Hong Kong coastal waters

During an investigation into the distribution of lignicolous marine fungi in Hong Kong coastal waters, pine blocks (Pinus massoniana Lambert) were used as one of the baiting substrates. The results from unscraped and scraped pine blocks showed that, in general, the presence of surface fouling organisms did not affect the pattern of occurrence of fungi either quantitatively or qualitatively. Apart from the presence of a few fungal species on the calcareous substrates provided by barnacles and shipworms, no other associations between fungi and fouling organisms were detected.     

The feeding ecology of little auks raises questions about winter zooplankton stocks in North Atlantic surface waters

Copepods are essential components of marine food webs worldwide. In the North Atlantic, they are thought to perform vertical migration and to remain at depths more than 500 m during winter. We challenge this concept through a study of the winter feeding ecology of little auks (Alle alle), a highly abundant planktivorous seabird from the North Atlantic. By combining stable isotope and behavioural analyses, we strongly suggest that swarms of copepods are still available to their predators in water surface layers (less than 50 m) during winter, even during short daylight periods. Using a new bioenergetic model, we estimate that the huge number (20–40 million birds) of little auks wintering off southwest Greenland consume 3600–7200 tonnes of copepods daily, strongly suggesting substantial zooplankton stocks in surface waters of the North Atlantic in the middle of the boreal winter.     

Distribution and biology of marine cladocerans in the coastal waters of southern China

Geographical and seasonal distributions of marine cladocerans in the coastal waters of southern China were studied. Penilia avirostris was the most common species, followed by Evadne tergestina and Podon schmackeri. P. avirostris and E. tergestina were most common during summer. P. schmackeri, found only in a small bay northeast of Hong Kong, showed no clear seasonal pattern of occurrence. P. avirostris and E. tergestina were found at temperatures ranging from 16–32°C and salinity ranging from 7.3–37.2. P. schmackeri was restricted to a temperature range of 17–29°C and a salinity range of 31.0–37.2. No significant relationships between marine cladoceran abundance and chlorophyll a concentration were found in samples taken from Tolo Harbour. Parthenogenetic brood size of P. avirostris and E. tergestina ranged from 1 to 14, while P. schmackeri was found to carry up to 19 embryos per brood. No geographical trend in fecundity patterns was observed. No correlation was found between body length and brood size. The occurrence of females with resting eggs was rare.     

Environmental DNA metabarcoding reveals winners and losers of global change in coastal waters

Studies of the ecological effects of global change often focus on one or a few species at a time. Consequently, we know relatively little about the changes underway at real-world scales of biological communities, which typically have hundreds or thousands of interacting species. Here, we use COI mtDNA amplicons from monthly samples of environmental DNA to survey 221 planktonic taxa along a gradient of temperature, salinity, dissolved oxygen and carbonate chemistry in nearshore marine habitat. The result is a high-resolution picture of changes in ecological communities using a technique replicable across a wide variety of ecosystems. We estimate community-level differences associated with time, space and environmental variables, and use these results to forecast near-term community changes due to warming and ocean acidification. We find distinct communities in warmer and more acidified conditions, with overall reduced richness in diatom assemblages and increased richness in dinoflagellates. Individual taxa finding more suitable habitat in near-future waters are more taxonomically varied and include the ubiquitous coccolithophore Emiliania huxleyi and the harmful dinoflagellate Alexandrium sp. These results suggest foundational changes for nearshore food webs under near-future conditions.     

A metagenomic assessment of microbial eukaryotic diversity in the global ocean

Surveying microbial diversity and function is accomplished by combining complementary molecular tools. Among them, metagenomics is a PCR free approach that contains all genetic information from microbial assemblages and is today performed at a relatively large scale and reasonable cost, mostly based on very short reads. Here, we investigated the potential of metagenomics to provide taxonomic reports of marine microbial eukaryotes. We prepared a curated database with reference sequences of the V4 region of 18S rDNA clustered at 97% similarity and used this database to extract and classify metagenomic reads. More than half of them were unambiguously affiliated to a unique reference whilst the rest could be assigned to a given taxonomic group. The overall diversity reported by metagenomics was similar to that obtained by amplicon sequencing of the V4 and V9 regions of the 18S rRNA gene, although either one or both of these amplicon surveys performed poorly for groups like Excavata, Amoebozoa, Fungi and Haptophyta. We then studied the diversity of picoeukaryotes and nanoeukaryotes using 91 metagenomes from surface down to bathypelagic layers in different oceans, unveiling a clear taxonomic separation between size fractions and depth layers. Finally, we retrieved long rDNA sequences from assembled metagenomes that improved phylogenetic reconstructions of particular groups. Overall, this study shows metagenomics as an excellent resource for taxonomic exploration of marine microbial eukaryotes.     

Distribution of biogenic silica and particulate organic matter in coastal and oceanic surface waters off the South Shetland Islands in summer

Biogenic silica (BSi), lithogenic silica (LSi), particiulate organic carbon (POC) and nitrogen (PON), and chlorophyll a (Chl a) concentration levels were measured in the surface waters (<100 m) off the northern coast of the South Shetland Islands in summer 1991. High concentration levels of BSi and LSi were recorded in the oceanic area and the coastal area, respectively. However, marked regional differences were not observed for POC, PON and Chl a concentrations. The mean BSi/POC atomic ratio (±SD) in the oceanic area (0.27±0.17) was 6 times that in the coastal area (0.045±0.020), except for the bloom situation (0.19±0.029). In contrast, the mean POC/PON atomic ratio was not significantly different in the coastal area (5.9±1.4) and the oceanic area (5.2±1.7). Nitzschia spp. were the dominant diatoms in the oceanic area but not in the coastal area. High BSi/POC ratios have been reported for blooms dominated by Nitzschia spp. even in the coastal regions of the Antarctic Ocean. The area difference in the BSi/POC ratios was probably related to the difference in species composition of phytoplankton and not to regional contrast. This species contributes significantly to high BSi/POC ratios in the Antarctic Ocean.