A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters

A metaproteomic survey of surface coastal waters near Palmer Station on the Antarctic Peninsula, West Antarctica, was performed, revealing marked differences in the functional capacity of summer and winter communities of bacterioplankton. Proteins from Flavobacteria were more abundant in the summer metaproteome, whereas winter was characterized by proteins from ammonia-oxidizing Marine Group I Crenarchaeota. Proteins prevalent in both seasons were from SAR11 and Rhodobacterales clades of Alphaproteobacteria, as well as many lineages of Gammaproteobacteria. The metaproteome data were used to elucidate the main metabolic and energy generation pathways and transport processes occurring at the microbial level in each season. In summer, autotrophic carbon assimilation appears to be driven by oxygenic photoautotrophy, consistent with high light availability and intensity. In contrast, during the dark polar winter, the metaproteome supported the occurrence of chemolithoautotrophy via the 3-hydroxypropionate/4-hydroxybutyrate cycle and the reverse tricarboxylic acid cycle of ammonia-oxidizing archaea and nitrite-oxidizing bacteria, respectively. Proteins involved in nitrification were also detected in the metaproteome. Taurine appears to be an important source of carbon and nitrogen for heterotrophs (especially SAR11), with transporters and enzymes for taurine uptake and degradation abundant in the metaproteome. Divergent heterotrophic strategies for Alphaproteobacteria and Flavobacteria were indicated by the metaproteome data, with Alphaproteobacteria capturing (by high-affinity transport) and processing labile solutes, and Flavobacteria expressing outer membrane receptors for particle adhesion to facilitate the exploitation of non-labile substrates. TonB-dependent receptors from Gammaproteobacteria and Flavobacteria (particularly in summer) were abundant, indicating that scavenging of substrates was likely an important strategy for these clades of Southern Ocean bacteria. This study provides the first insight into differences in functional processes occurring between summer and winter microbial communities in coastal Antarctic waters, and particularly highlights the important role that ‘dark'' carbon fixation has in winter.     

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。     

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.     

Diversity of bacterioplankton in coastal seawaters of Fildes Peninsula,King George Island,Antarctica

The bacterioplankton not only serves critical functions in marine nutrient cycles, but can also serve as indicators of the marine environment. The compositions of bacterial communities in the surface seawater of Ardley Cove and Great Wall Cove were analyzed using a 16S rRNA multiplex 454 pyrosequencing approach. Similar patterns of bacterial composition were found between the two coves, in which Bacteroidetes, Alphaproteobacteria, and Gammaproteobacteria were the dominant members of the bacterioplankton communities. In addition, a large fraction of the bacterial sequence reads (on average 5.3 % per station) could not be assigned below the domain level. Compared with Ardley Cove, Great Wall Cove showed higher chlorophyll and particulate organic carbon concentrations and exhibited relatively lower bacterial richness and diversity. Inferred metabolisms of summer bacterioplankton in the two coves were characterized by chemoheterotrophy and photoheterotrophy. Results suggest that some cosmopolitan species (e.g., Polaribacter and Sulfitobacter) belonging to a few bacterial groups that usually dominate in marine bacterioplankton communities may have similar ecological functions in similar marine environments but at different geographic locations.     

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.     

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.     

Seasonal microbial community dynamics correlate with phytoplankton-derived polysaccharides in surface coastal waters

Phytoplankton produce large amounts of polysaccharide gel material known as transparent exopolymer particles (TEP). We investigated the potential links between phytoplankton-derived TEP and microbial community structure in the sea surface microlayer and underlying water at the English Channel time-series station L4 during a spring diatom bloom, and in two adjacent estuaries. Major changes in bacterioneuston and bacterioplankton community structure occurred after the peak of the spring bloom at L4, and coincided with the significant decline of microlayer and water column TEP. Increased abundance of Flavobacteriales and Rhodobacterales in bacterioneuston and bacterioplankton communities at L4 was significantly related to the TEP decline, indicating that both taxa could be responsible. The results suggest that TEP is an important factor in determining microbial diversity in coastal waters, and that TEP utilisation could be a niche occupied by Flavobacteriales and Rhodobacterales.     

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     

Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems

In order to extend previous comparisons between coastal marine bacterioplankton communities and their open ocean and freshwater counterparts, here we summarize and provide new data on a clone library of 105 SSU rRNA genes recovered from seawater collected over the western continental shelf of the USA in the Pacific Ocean. Comparisons to previously published data revealed that this coastal bacterioplankton clone library was dominated by SSU rRNA gene phylotypes originally described from surface waters of the open ocean, but also revealed unique SSU rRNA gene lineages of beta Proteobacteria related to those found in clone libraries from freshwater habitats. beta Proteobacteria lineages common to coastal and freshwater samples included members of a clade of obligately methylotrophic bacteria, SSU rRNA genes affiliated with Xylophilus ampelinus, and a clade related to the genus Duganella. In addition, SSU rRNA genes were recovered from such previously recognized marine bacterioplankton SSU rRNA gene clone clusters as the SAR86, SAR11, and SAR116 clusters within the class Proteobacteria, the Roseobacter clade of the alpha subclass of the Proteobacteria, the marine group A/SAR406 cluster, and the marine Actinobacteria clade. Overall, these results support and extend previous observations concerning the global distribution of several marine planktonic prokaryote SSU rRNA gene phylotypes, but also show that coastal bacterioplankton communities contain SSU rRNA gene lineages (and presumably bacterioplankton) shown previously to be prevalent in freshwater habitats.     

Differential responses to UVR by bacterioplankton and phytoplankton from the surface and the base of the mixed layer

SUMMARY 1. We tested the influence of ultraviolet radiation (UVR) and shallow stratification on phytoplankton and bacterioplankton from the surface and the base of the mixed layer in two boreal lakes in north-western Ontario, Canada.
2. We measured phytoplankton biomass and production, bacterioplankton production and plankton respiration after transplantation under three solar radiation treatments: ambient radiation (Photosynthetically active radiation (PAR) + ultraviolet-A (UVA) + ultraviolet-B (UVB)), minus UVB (PAR + UVA) and PAR only. We repeated this experiment on three occasions in each lake during the summer.
3. Solar stress (measured as reduced growth and photoinhibition) was generally only found in the 'base phytoplankton' (i.e. originating from the base of the mixed layer). No inhibition of photosynthesis by UVB exposure was found in near-surface phytoplankton. On the other hand, production of near-surface bacterioplankton was reduced following a 4-h UVR exposure but had increased after a 48-h exposure to both UVA and UVB compared with the PAR only treatment.
4. Negative effects of UVR on phytoplankton and bacterioplankton were not ubiquitous. We emphasise the importance of conducting experiments repeatedly, particularly those which test the effects of UVR on different community assemblages from different lakes.     

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.     

Microzooplankton herbivory and bacterivory in Newfoundland coastal waters during spring, summer and winter

Grazing by microzooplankton on autotrophic and heterotrophicpicoplankton as well as >0.7 µm phytoplankton (as measuredby chlorophyll a) was quantified during July, August, October,January and April in the surface layer of Logy Bay, Newfoundland(47°38'14'N, 52°39'36'W). Rates of growth and grazingmortality of bacteria, Synechococcus and >0.7 µm phytoplanktonwere measured using the sea water dilution technique. Microzooplanktoningested 83–184, 96–366 and 64–118% of bacterial,Synechococcus and >0.7 µm phytoplankton daily potentialproduction, respectively and 34–111, 25–30 and 16–131%of bacterial, Synechococcus and >0.7 µm phytoplanktonstanding stocks, respectively. The trends in prey net growthrates followed the seasonal cycles of prey biomass, suggestingthat microzooplankton are important grazers in Newfoundlandcoastal waters. Ingestion was lowest during January and October(~2 µg C l^–1 day^–1) and highest in August(~20 µg C l^–1 day^–1). Aside from April when>0.7 µm phytoplankton represented the majority (~80%)of carbon ingested, bacterioplankton and <1 µm phytoplanktonrepresented most of the carbon ingested (~40–100%). Althoughmicrozooplankton have here-to-fore been unrecognized as an importantgrazer population in Newfoundland coastal waters, these resultssuggest that they play an important role in carbon flow withinthe pelagic food web, even at low temperatures in Logy Bay.     

Relationship between bacterioplankton and phytoplankton community dynamics during late spring and early summer in Lake Taihu, China

The relationship between bacterioplankton and phytoplankton community compositions was investigated from April to June, 2005 with samples taken at five different stations in Lake Taihu, China. Bacterioplankton and phytoplankton community compositions as determined by denaturing gradient gel electrophoresis of polymerase chain reaction amplified bacterial 16S rRNA gene fragments (PCR-DGGE) and microscopic examination, respectively, revealed a high degree of diversity. In total, 43 unique bands were identified amongst the DGGE profiles, and 29 dominant phytoplankton populations were observed. The DGGE profiles were clustered into two distinct groups. These two clusters were closely associated with two dominant phytoplanktons, Ulothrix sp. and Microcystis spp., as observed on April 19, May 27 and June 27, 2005, respectively. The relationship between bacterioplankton and phytoplankton community compositions was investigated using Canonical Correspondence Analysis (CCA) with the Shannon-Wiener diversity index of phytoplankton community (Hp), the total cell abundance of phytoplankton (N) and the relative abundance of Microcystis spp. (M) as the variables. The CCA results indicated a 30.9 % correlation coefficient, suggesting a high degree of correlation between bacterioplankton and phytoplankton community compositions.     

Relationship between bacterioplankton and phytoplankton community dynamics during late spring and early summer in Lake Taihu, China

The relationship between bacterioplankton and phytoplankton community compositions was investigated from April to June, 2005 with samples taken at five different stations in Lake Taihu, China. Bacterioplankton and phytoplankton community compositions as determined by denaturing gradient gel electrophoresis of polymerase chain reaction amplified bacterial 16S rRNA gene fragments (PCR-DGGE) and microscopic examination, respectively, revealed a high degree of diversity. In total, 43 unique bands were identified amongst the DGGE profiles, and 29 dominant phytoplankton populations were observed. The DGGE profiles were clustered into two distinct groups. These two clusters were closely associated with two dominant phytoplanktons, Ulothrix sp. and Microcystis spp., as observed on April 19, May 27 and June 27, 2005, respectively. The relationship between bacterioplankton and phytoplankton community compositions was investigated using Canonical Correspondence Analysis (CCA) with the Shannon-Wiener diversity index of phytoplankton community (Hp), the total cell abundance of phytoplankton (N) and the relative abundance of Microcystis spp. (M) as the variables. The CCA results indicated a 30.9 % correlation coefficient, suggesting a high degree of correlation between bacterioplankton and phytoplankton community compositions.     

珠江口城市段近岸表层水体浮游细菌分离方法比较

为了更好地分离珠江口未/难培养的浮游细菌,本研究以珠江河口三个样点的水体为研究对象,同时采用了纯培养和免培养的方法,对不同培养基的分离效果进行了探索。在纯培养实验中,本研究选择了7种不同的分离培养基,共分离获得153株菌;同时,将扩增子分析结果作为分离效果的参考,所有环境样品中共包含3 553个操作分类单元（operational taxonomic units,OTUs）。对三个样点微生物类群的多样性进行比较,纯培养结果显示珠江口下游珠海样点多样性最高,其次为中大和虎门样点;免培养则显示虎门样点多样性最高;对比7种不同的分离培养基,Z7（R₂A）培养基的分离效果最好,分离菌株数和分离类群的α多样性最高,Z1（改良ISP 2）次之;主坐标分析结合韦恩图的结果表明相比其余的培养基,Z1和Z7培养基分离获得的菌群兼具普遍性和特异性,进一步证明了这两种培养基的分离效果较佳;冗余分析结果表明K₂HPO₄、酵母粉、可溶性淀粉、MgSO₄·7H₂O、麦芽膏和葡萄糖与特定类群的分离有相关关系,其中K₂HPO₄的影响最为显著（P<0.05）。本文通过7种不同培养基对河口微生物分离效果的探究,有助于我们在研究未知微生物的营养特性时,选择成分和组成更合理的培养基来提升河口微生物纯培养的分离效率。     

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.     

浙闽沿海生态牧场技术示范区浮游细菌群落和功能的时空变化

【目的】本文通过不同季节的4个航次调查研究了2个浙闽沿海生态牧场技术示范区的浮游细菌群落的变化,揭示了示范区菌群结构的时空变化,探究其对于海洋生态系统的潜在影响。【方法】使用16SrRNA基因扩增子测序技术,对2个示范区4个季节航次共128个样点中浮游细菌的16SrRNA基因V4区序列进行测序,并通过分析其组成和多样性,借助FAPROTAX功能预测,分析不同季节和示范区浮游细菌的差异。【结果】128个样品量化后共获得2510976条优质序列,2个示范区的主要优势浮游细菌类群均为α变形菌纲、γ变形菌纲、β变形菌纲、放线菌纲、黄杆菌纲等,2个示范区浮游细菌的α多样性指数随季节演替而产生波动,且大多数环境因子都与其具有显著相关性;浙闽沿海浮游细菌的群落构建过程随时空变化而产生差异,扩散限制是2个示范区浮游细菌群落构建过程中占比最大的生态过程(除台山岛示范区秋季),2个示范区多数季节的浮游细菌群落相似性基于Bray-Curtis的地理距离衰减印证了这一点;基于FAPROTAX功能预测得到的2个示范区浮游细菌的功能以化能异养和氮硫循环为主,从一定程度上与当地的环境因子变化相关联。【结论】浙闽沿海...