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.     

The phylogenetic affiliation of an uncultured population of ammonia-oxidizing bacteria harboring environmental sequences of amoA cluster-3

We investigated the phylogenetic diversity of ammonia-oxidizing bacteria (AOB) in Yellow Sea continental shelf sediment by the cloning and sequencing of PCR-amplified amoA and 16S rRNA genes. Phylogenetic analysis of the amoA-related clones revealed that the diversity of AOB was extremely low at the study site. The majority (92.7%) of amoA clones obtained belonged to a single cluster, environmental amoA cluster-3, the taxonomic position of which was previously unknown. Phylogenetic analysis on AOB-specific 16S rRNA gene sequences also demonstrated a very low diversity. All of the cloned 16S rRNA gene sequences comprised a single phylotype that belonged to the members of uncultured Nitrosospira cluster-1, suggesting that AOB belonging to the uncultured Nitrosospira cluster- 1 could carry amoA sequences of environmental amoA cluster-3.     

Patterns of marine bacterioplankton biodiversity in the surface waters of the Scotia Arc, Southern Ocean

Spatial patchiness in marine surface bacterioplankton populations was investigated in the Southern Ocean, where the Antarctic Circumpolar Current meets the islands of the Scotia Arc and is subjected to terrestrial input, upwelling of nutrients and seasonal phytoplankton blooms. Total bacterioplankton population density, group-specific taxonomic distribution and six of eight dominant members of the bacterioplankton community were found to be consistent across 18 nearshore sites at eight locations around the Scotia Arc. Results from seven independent 16S rRNA gene clone libraries (1223 sequences in total) and fluorescent in situ hybridization suggested that microbial assemblages were predominantly homogeneous between Scotia Arc sites, where the Alphaproteobacteria, Gammaproteobacteria and the Cytophaga-Flavobacterium-Bacteroidetes cluster were the dominant bacterial groups. Of the 1223 useable sequences generated, 1087 (89%) shared ≥?97% similarity with marine microorganisms and 331 (27%) matched published sequences previously detected in permanently cold Arctic and Antarctic marine environments. Taken together, results suggest that the dominant bacterioplankton groups are consistent between locations, but significant differences may be detected across the rare biodiversity.     

Winter distribution of four species of the genus Ceratium from Cape Canaveral, Florida to Cape Henlopen, Delaware

Surface plankton tows with a modified 3/4 m Nansen net weremade along the east coast of the United States from Cape Canaveral,Florida to Cape Henlopen, Delaware. The armoured dinoflagellatesin the surface layer were found to form two distinct assemblages.The assemblage north of Cape Hatteras was composed exclusivelyof Ceratium tripos and C. macroceras. South of Cape Hatteras,except for an intrusion of Virginian Shelf Water into RayleighBay, the armoured dinoflagellates present in greatest numberswere C. trichoceras and C. massiliense. The two northern specieswere also present. In the warm oceanic and shelf waters southof Cape Hatteras, there were many tintinnids and foraminiferansin addition to the armoured dinoflagellates. The distributionpattern was in good agreement with high resolution infraredsatellite imagery of the Gulf Stream position off Cape Hatterasduring the sampling period.     

Microbial community dynamics in a humic lake: differential persistence of common freshwater phylotypes

In an effort to better understand the factors contributing to patterns in freshwater bacterioplankton community composition and diversity, we coupled automated ribosomal intergenic spacer analysis (ARISA) to analysis of 16S ribosomal RNA (rRNA) gene sequences to follow the persistence patterns of 46 individual phylotypes over 3 years in Crystal Bog Lake. Additionally, we sought to identify linkages between the observed phylotype variations and known chemical and biological drivers. Sequencing of 16S rRNA genes obtained from the water column indicated the presence of phylotypes associated with the Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, TM7 and Verrucomicrobia phyla, as well as phylotypes with unknown affiliation. Employment of the 16S rRNA gene/ARISA method revealed that specific phylotypes varied independently of the entire bacterial community dynamics. Actinobacteria, which were present on greater than 95% of sampling dates, did not share the large temporal variability of the other identified phyla. Examination of phylotype relative abundance patterns (inferred using ARISA fragment relative fluorescence) revealed a strong correlation between the dominant phytoplankton succession and the relative abundance patterns of the majority of individual phylotypes. Further analysis revealed covariation among unique phylotypes, which formed several distinct bacterial assemblages correlated with particular phytoplankton communities. These data indicate the existence of unique persistence patterns for different common freshwater phylotypes, which may be linked to the presence of dominant phytoplankton species.     

Temporal patterns of microbial community structure in the Mid-Atlantic Bight

Although open ocean time-series sites have been areas of microbial research for years, relatively little is known about the population dynamics of bacterioplankton communities in the coastal ocean on kilometer spatial and seasonal temporal scales. To gain a better understanding of microbial community variability, monthly samples of bacterial biomass were collected in 1995-1996 along a 34-km transect near the Long-Term Ecosystem Observatory (LEO-15) off the New Jersey coast. Surface and bottom sampling was performed at seven stations along a transect line with depths ranging from 1 to 35 m (n=178). Microbial populations were fingerprinted using ribosomal 16S rRNA genes and terminal restriction fragment length polymorphism analysis. Results from cluster analysis revealed distinct temporal patterns among the bacterioplankton communities in the Mid-Atlantic Bight rather than grouping by sample location or depth. Principal components analysis models supported the temporal patterns. In addition, partial least squares regression modeling could not discern a significant correlation from traditional oceanographic physical and phytoplankton nutrient parameters on overall bacterial community variability patterns at LEO-15. These results suggest factors not traditionally measured during oceanographic studies are structuring coastal microbial communities.     

Coherent dynamics and association networks among lake bacterioplankton taxa

Bacteria have important roles in freshwater food webs and in the cycling of elements in the ecosystem. Yet specific ecological features of individual phylogenetic groups and interactions among these are largely unknown. We used 454 pyrosequencing of 16S rRNA genes to study associations of different bacterioplankton groups to environmental characteristics and their co-occurrence patterns over an annual cycle in a dimictic lake. Clear seasonal succession of the bacterioplankton community was observed. After binning of sequences into previously described and highly resolved phylogenetic groups (tribes), their temporal dynamics revealed extensive synchrony and associations with seasonal events such as ice coverage, ice-off, mixing and phytoplankton blooms. Coupling between closely and distantly related tribes was resolved by time-dependent rank correlations, suggesting ecological coherence that was often dependent on taxonomic relatedness. Association networks with the abundant freshwater Actinobacteria and Proteobacteria in focus revealed complex interdependencies within bacterioplankton communities and contrasting linkages to environmental conditions. Accordingly, unique ecological features can be inferred for each tribe and reveal the natural history of abundant cultured and uncultured freshwater bacteria.     

太湖浮游细菌与春末浮游藻类群落结构演替的相关分析

为研究浮游细菌与浮游藻类群落演替的相关性,2005年4月至6月在太湖5个观测点采集浮游细菌及浮游藻类样本。分别采用聚合酶链式反应-变性梯度凝胶电泳（PCR—DGGE）和显微观察的方法分析浮游细菌及浮游藻类群落组成。结果表明,春末夏初,浮游细菌与藻类均呈现较高的多样性,浮游细菌DGGE图谱具有43种不同条带,浮游藻类的常见种有29种。浮游细菌群落聚类分析显示,丝藻（Ulothrix sp．）和微囊藻（Microcystis spp．）占优势时,浮游细菌群落基因组成存在明显差异。以藻类种群Shannon—Wiener多样性指数（Hp）,浮游藻类总细胞数（N）以及Microcystis spp．（M）百分含量为变量,典型对应分析（CCA）结果显示浮游细菌与浮游藻类群落结构变化的相关系数为30．9％,表明春末夏初太湖浮游细菌与浮游藻类群落演替具有较高的相关性。     

Changes in bacterioplankton composition under different phytoplankton regimens

The results of empirical studies have revealed links between phytoplankton and bacterioplankton, such as the frequent correlation between chlorophyll a and bulk bacterial abundance and production. Nevertheless, little is known about possible links at the level of specific taxonomic groups. To investigate this issue, seawater microcosm experiments were performed in the northwestern Mediterranean Sea. Turbulence was used as a noninvasive means to induce phytoplankton blooms dominated by different algae. Microcosms exposed to turbulence became dominated by diatoms, while small phytoflagellates gained importance under still conditions. Denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments showed that changes in phytoplankton community composition were followed by shifts in bacterioplankton community composition, both as changes in the presence or absence of distinct bacterial phylotypes and as differences in the relative abundance of ubiquitous phylotypes. Sequencing of DGGE bands showed that four Roseobacter phylotypes were present in all microcosms. The microcosms with a higher proportion of phytoflagellates were characterized by four phylotypes of the Bacteroidetes phylum: two affiliated with the family Cryomorphaceae and two with the family Flavobacteriaceae. Two other Flavobacteriaceae phylotypes were characteristic of the diatom-dominated microcosms, together with one Alphaproteobacteria phylotype (Roseobacter) and one Gammaproteobacteria phylotype (Methylophaga). Phylogenetic analyses of published Bacteroidetes 16S rRNA gene sequences confirmed that members of the Flavobacteriaceae are remarkably responsive to phytoplankton blooms, indicating these bacteria could be particularly important in the processing of organic matter during such events. Our data suggest that quantitative and qualitative differences in phytoplankton species composition may lead to pronounced differences in bacterioplankton species composition.     

Phylogeny and spatio‐temporal diversification of Prunus subgenus Laurocerasus section Mesopygeum (Rosaceae) in the Malesian region

The goals of this study were to reconstruct the phylogeny of Prunus subgenus Laurocerasus section Mesopygeum and to provide a preliminary assessment of its spatio‐temporal diversification in the Malesian region. We inferred the phylogeny using nuclear ITS and ETS and plastid psbA‐trnH, rps16, rpl16, and trnC‐petN sequences. Our analyses support the monophyly of sect. Mesopygeum. Within sect. Mesopygeum, we identified four main subclades: (i) Prunus lancilimba from continental Asia; (ii) Prunus ruthii from Malay Peninsula; (iii) a subclade comprising species from areas centered on the Sunda shelf and also a few species from continental Asia and Wallacea; and (iv) a subclade composed of species from areas of the Sahul shelf, with a small number of taxa also from areas of the Sunda shelf, continental Asia, and the Philippines. We estimated that sect. Mesopygeum originated in continental Asia at c. 44.71 Mya (95% HPD: 31.66–46.90). Nine dispersals between major geographic areas were inferred. From continental Asia, three and two dispersals were inferred to the Sunda shelf and the Sahul shelf in the mid‐Oligocene, respectively. Two dispersals were inferred from the Sahul shelf region to the Sunda shelf in late Oligecene and early Miocene, respectively. There were also two dispersals inferred from the Sunda shelf region, one to the Philippines and one to Wallacea, in the middle and late Miocene, respectively. The diversification in sect. Mesopygeum was likely driven by active geologic events and orogenies in the Neogene in the Malesian region.     

Phylogenetic diversity of winter bacterioplankton of eutrophic siberian reservoirs as revealed by 16S rRNA gene sequence

Using 16S rRNA gene sequence analyses we investigated the bacterial diversity of winter bacterioplankton of two eutrophic Siberian reservoirs. These reservoirs show similarity in phytoplankton community composition in spring and autumn but tend to differ in summer in exhibiting cyanobacterial bloom. Forty-eight unique partial 16S RNA gene sequences retrieved from two libraries were mostly affiliated with the class Actinobacteria, b subdivision of the class Proteobacteria, and the phylum Cytophaga-Flavobacterium-Bacteroides. The clone library of the pond exhibiting summer cyanobacterial bloom showed more diversity in sequence composition. A significant number of bacterial 16S rRNA gene clones were closely related to freshwater bacteria previously found in different aquatic ecosystems. This finding confirms the assumption that some bacterial clades are globally distributed.     

Seasonal dynamics of bacterioplankton community structure in a eutrophic lake as determined by 5S rRNA analysis.

Community structure of bacterioplankton was studied during the major growth season for phytoplankton (April to October) in the epilimnion of a temperate eutrophic lake (Lake Plusssee, northern Germany) by using comparative 5S rRNA analysis. Estimates of the relative abundances of single taxonomic groups were made on the basis of the amounts of single 5S rRNA bands obtained after high-resolution electrophoresis of RNA directly from the bacterioplankton. Full-sequence analysis of single environmental 5S rRNAs enabled the identification of single taxonomic groups of bacteria. Comparison of partial 5S rRNA sequences allowed the detection of changes of single taxa over time. Overall, the whole bacterioplankton community showed two to eight abundant (>4% of the total 5S rRNA) taxa. A distinctive seasonal succession was observed in the taxonomic structure of this pelagic community. A rather-stable community structure, with seven to eight different taxonomic units, was observed beginning in April during the spring phytoplankton bloom. A strong reduction in this diversity occurred at the beginning of the clear-water phase (early May), when only two to four abundant taxa were observed, with one taxon dominating (up to 72% of the total 5S rRNA). The community structure during summer stagnation (June and July) was characterized by frequent changes of different dominating taxa. During late summer, a dinoflagellate bloom (Ceratium hirudinella) occurred, with Comamonas acidovorans (beta-subclass of the class Proteobacteria) becoming the dominant bacterial species (average abundance of 43% of the total 5S rRNA). Finally, the seasonal dynamics of the community structure of bacterioplankton were compared with the abundances of other major groups of the aquatic food web, such as phyto- and zooplankton, revealing that strong grazing pressure by zooplankton can reduce microbial diversity substantially in pelagic environments.     

Comparison of phytoplankton concentrations and cell volume measurements from the continental shelf off Cape Cod,Massachusetts, U.S.A.

Phytoplankton composition and concentrations varied at stations across the shelf with maximum phytoplankton volumes not necessarily related to maximum concentration values. The shelf phytoplankton off Cape Cod, Massachusetts was composed of two major size classes: the ultraplankton (cells less than 10 microns in size), and net phytoplankton. Cell concentrations decreased along transects seaward, to increase near the shelf margin. Higher cell volume values coincided with increased cell counts east of Cape Cod, but were lower southward, increasing in the mid-shelf region, to decrease along the shelf margin. The shelf ultraplankton component typically represented over 90% of the standing crop, but less than 1% of its phytovolume. Associations are made between cell volumes and concentration combinations and different phytoplankton assemblages.     

Community composition of the marine bacterioplankton in Kongsfjorden (Spitsbergen) as revealed by 16S rRNA gene analysis

Phylogenetic diversity of the marine bacterioplankton in Kongsfjorden (Spitsbergen) was investigated by 16S rRNA gene analysis. Community fingerprint analysis by PCR-denaturing gradient gel electrophoresis revealed that there was no apparent difference of bacterioplankton community composition between sampling locations in the fjord. A higher biodiversity was observed in bottom water of station 3 in the central part of the fjord. By 16S rRNA gene clone library analysis, sequences detected both in surface and bottom water of station 3 fell into eight putative divisions, including Proteobacteria (Alpha, Beta, Gamma and Delta), Bacteroidetes, Actinobacteria, Verrucomicrobia and unidentified bacteria, in addition to chloroplasts of algae. Sequences representing Planctomycetes were only observed in bottom water. Compared to the preponderance of clones representing Gammaproteobacteria (36.5%) and Alphaproteobacteria (29.4%) in bottom water, Alphaproteobacteria (43.6%) and algae (27.7%) constituted two dominant fractions in surface water. Cloned sequences showed 82.1–100% similarity to those described sequences. It suggests that, attributing to the influence of ocean currents as well as freshwater input in the summer, the bacterial community in Kongsfjorden may consist of a mixture of cosmopolitan and uniquely endemic phylotypes.     

Changes in bacterioplankton community structure and activity with depth in a eutrophic lake as revealed by 5S rRNA analysis

The community structure of bacterioplankton was studied at different depths (0 to 25 m) of a temperate eutrophic lake (Lake Plusssee in northern Germany) by using comparative 5S rRNA analysis. The relative amounts of taxonomic groups were estimated from 5S rRNA bands separated by high-resolution electrophoresis. Comparison of partial 5S rRNA sequences enabled detection of changes in single taxa over space and during seasons. Overall, the bacterioplankton community was dominated by 3 to 14 abundant (>4% of the total 5S rRNA) taxa. In general, the number of 5S rRNA bands (i.e., the number of bacterial taxa) decreased with depth. In the fall, when thermal stratification and chemical stratification were much more pronounced than they were in the spring, the correlation between the depth layers and the community structure was more pronounced. Therefore, in the fall each layer had its own community structure; i.e., there were different community structures in the epilimnion, the metalimnion, and the hypolimnion. Only three 5S rRNA bands were detected in the hypolimnion during the fall, and one band accounted for about 70% of the total 5S rRNA. The sequences of individual 5S rRNA bands from the spring and fall were different for all size classes analyzed except two bands, one of which was identified as Comamonas acidivorans. In the overall analysis of the depth profiles, the diversity in the epilimnion contrasted with the reduced diversity of the bacterioplankton communities in the hypolimnion, and large differences occurred in the composition of the epilimnion at different seasons except for generalists like C. acidivorans.     

Bacterial and phytoplankton responses to nutrient amendments in a boreal lake differ according to season and to taxonomic resolution

Nutrient limitation and resource competition in bacterial and phytoplankton communities may appear different when considering different levels of taxonomic resolution. Nutrient amendment experiments conducted in a boreal lake on three occasions during one open water season revealed complex responses in overall bacterioplankton and phytoplankton abundance and biovolume. In general, bacteria were dominant in spring, while phytoplankton was clearly the predominant group in autumn. Seasonal differences in the community composition of bacteria and phytoplankton were mainly related to changes in observed taxa, while the differences across nutrient treatments within an experiment were due to changes in relative contributions of certain higher- and lower-level phylogenetic groups. Of the main bacterioplankton phyla, only Actinobacteria had a treatment response that was visible even at the phylum level throughout the season. With increasing resolution (from 75 to 99% sequence similarity) major responses to nutrient amendments appeared using 454 pyrosequencing data of 16S rRNA amplicons. This further revealed that OTUs (defined by 97% sequence similarity) annotated to the same highly resolved freshwater groups appeared to occur during different seasons and were showing treatment-dependent differentiation, indicating that OTUs within these groups were not ecologically coherent. Similarly, phytoplankton species from the same genera responded differently to nutrient amendments even though biovolumes of the majority of taxa increased when both nitrogen and phosphorus were added simultaneously. The bacterioplankton and phytoplankton community compositions showed concurrent trajectories that could be seen in synchronous succession patterns over the season. Overall, our data revealed that the response of both communities to nutrient changes was highly dependent on season and that contradictory results may be obtained when using different taxonomic resolutions.     

High level of bacterial diversity and novel taxa in continental shelf sediment

The bacterial diversity of the continental shelf sediment in the Yellow Sea was investigated by the cloning and sequencing of PCR-amplified 16S rRNA genes. The majority of the cloned sequences were distinct phylotypes that were novel at the species level. The richness estimator indicated that the sediment sample might harbor up to 32 phylum-level taxa. A large number of low-abundance, phylum-level taxa accounted for most of the observed phylogenetic diversity at our study site, suggesting that these low-abundance taxa might play crucial roles in the shelf sediment ecosystem.     

High temporal but low spatial heterogeneity of bacterioplankton in the Chesapeake Bay

Compared to freshwater and the open ocean, less is known about bacterioplankton community structure and spatiotemporal dynamics in estuaries, particularly those with long residence times. The Chesapeake Bay is the largest estuary in the United States, but despite its ecological and economic significance, little is known about its microbial community composition. A rapid screening approach, ITS (internal transcribed spacer)-LH (length heterogeneity)-PCR, was used to screen six rRNA operon (16S rRNA-ITS-23S rRNA) clone libraries constructed from bacterioplankton collected in three distinct regions of the Chesapeake Bay over two seasons. The natural length variation of the 16S-23S rRNA gene ITS region, as well as the presence and location of tRNA-alanine coding regions within the ITS, was determined for 576 clones. Clones representing unique ITS-LH-PCR sizes were sequenced and identified. Dramatic shifts in bacterial composition (changes within subgroups or clades) were observed for the Alphaproteobacteria (Roseobacter clade, SAR11), Cyanobacteria (Synechococcus), and Actinobacteria, suggesting strong seasonal variation within these taxonomic groups. Despite large gradients in salinity and phytoplankton parameters, a remarkably homogeneous bacterioplankton community was observed in the bay in each season. Stronger seasonal, rather than spatial, variation of the bacterioplankton population was also supported by denaturing gradient gel electrophoresis and LH-PCR analyses, indicating that environmental parameters with stronger seasonal, rather than regional, dynamics, such as temperature, might determine bacterioplankton community composition in the Chesapeake Bay.