Spatio-temporal variability and diversity of water column prokaryotic communities in the eastern North Atlantic

Intensified nitrogen removal in constructed wetlands by novel spray aeration system and different influent COD/N ratios

The degradation performance of organic matters and microorganism abundance variations of two horizontal subsurface flow constructed wetlands (HSSFCWs) with different influent COD/N ratios and a spray aeration system were investigated. Oxygen-enriched influent water was beneficial to enhance the abilities of nitrification and biodegradation of organic matters. Due to the sufficient carbon source supply under influent COD/N ratio of 8.0, the high removal performances of COD (93%), NH₄-N (85%) and total nitrogen (78%) were simultaneously obtained in HSSFCWs with a spray aeration system. The increase in nitrite and nitrate bacteria was beneficial to complete nitrification and improve NH₄-N removal. The increase in denitrifying bacteria contributed to complete denitrification and guaranteed the high removal efficiency of NO₃-N. The results suggested that the spray aeration combined with high influent COD/N ratios could achieve the high nitrogen removal in HSSFCWs.

An improved device with an affinity membrane to collect depth specific contamination free water for environmental assessment

The prime requirement for marine water studies is a competent sampling device that can collect water samples perfectly without any contamination to avoid false analysis.

Optical properties of dissolved organic matter relate to different depth-specific patterns of archaeal and bacterial community structure in the North Atlantic Ocean

Prokaryotic abundance, activity and community composition were studied in the euphotic, intermediate and deep waters off the Galician coast (NW Iberian margin) in relation to the optical characterization of dissolved organic matter (DOM). Microbial (archaeal and bacterial) community structure was vertically stratified. Among the Archaea, Euryarchaeota, especially Thermoplasmata, was dominant in the intermediate waters and decreased with depth, whereas marine Thaumarchaeota, especially Marine Group I, was the most abundant archaeal phylum in the deeper layers. The bacterial community was dominated by Proteobacteria through the whole water column. However, Cyanobacteria and Bacteroidetes occurrence was considerable in the upper layer and SAR202 was dominant in deep waters. Microbial composition and abundance were not shaped by the quantity of dissolved organic carbon, but instead they revealed a strong connection with the DOM quality. Archaeal communities were mainly related to the fluorescence of DOM (which indicates respiration of labile DOM and generation of refractory subproducts), while bacterial communities were mainly linked to the aromaticity/age of the DOM produced along the water column. Taken together, our results indicate that the microbial community composition is associated with the DOM composition of the water masses, suggesting that distinct microbial taxa have the potential to use and/or produce specific DOM compounds.

Vertical profiles of bacteria in the tropical and subarctic oceans revealed by pyrosequencing

Community composition of Bacteria in the surface and deep water layers were examined at three oceanic sites in the Pacific Ocean separated by great distance, i.e., the South China Sea (SCS) in the western tropical Pacific, the Costa Rica Dome (CRD) in the eastern tropical Pacific and the western subarctic North Pacific (SNP), using high throughput DNA pyrosequencing of the 16S rRNA gene. Bioinformatic analysis rendered a total of 143600 high quality sequences with an average 11967 sequences per sample and mean read length of 449 bp. Phylogenetic analysis showed that Proteobacteria dominated in all shallow and deep waters, with Alphaproteobacteria and Gammaproteobacteria the two most abundant components, and SAR11 the most abundant group at family level in all regions. Cyanobacteria occurred mainly in the surface euphotic layer, and the majority of them in the tropical waters belonged to the GpIIa family including Prochlorococcus and Synechococcus, whilst those associated with Cryptophytes and diatoms were common in the subarctic waters. In general, species richness (Chao1) and diversity (Shannon index H') were higher for the bacterial communities in the intermediate water layers than for those in surface and deep waters. Both NMDS plot and UPGMA clustering demonstrated that bacterial community composition in the deep waters (500 m ~2000 m) of the three oceanic regions shared a high similarity and were distinct from those in the upper waters (5 m ~100 m). Our study indicates that bacterial community composition in the DOC-poor deep water in both tropical and subarctic regions were rather stable, contrasting to those in the surface water layers, which could be strongly affected by the fluctuations of environmental factors.

Spatio-temporal diversity of free-living and particle-attached prokaryotes in the tropical lagoon of Ahe atoll (Tuamotu Archipelago) and its surrounding oceanic waters

Spatio-temporal variability of prokaryotic water column communities inside and outside a Polynesian tropical lagoon subjected to pearl oysters farming was assessed in terms of abundance by quantitative PCR and diversity by DGGE. Communities and operational taxonomic units (OTUs) were analysed according to dry/rainy seasons and free-living/particle-attached state. Bacterial density was higher in the lagoon compared to ocean and a seasonal trend was observed. No influence of the localisation within lagoon or of the planktonic/attached states was noticed on bacterial abundance and diversity. The OTUs belonged to Cyanobacteria, to heterotrophic groups in Proteobacteria and Flavobacteria. Archaeal abundance showed seasonal tendency and particle-prevalence, but no effect of lagoon or oceanic location was observed. Lagoon and oceanic archaeal diversity were different and Euryarchaeota (MG-II, MBG, and Halobacteria) were detected. During the dry season, planktonic and particle-associated community differed, whereas at rainy season, both communities were similar and included members usually associated with coral.

Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep-ocean environment

Relatively little information is available for the composition of microbial communities present in hadal environments, the deepest marine locations. Here we present a description of the phylogenetic diversity of particle-associated (> 3 µm) and free-living (3-0.22 µm) microorganisms present in a pelagic trench environment. Small subunit ribosomal RNA gene sequences were recovered from members of the Bacteria, Archaea and Eukarya obtained from a depth of 6000 m in the Puerto Rico Trench (PRT). Species richness estimates for the bacterial particle-associated fraction were greater compared with the free-living fraction and demonstrated statistically significant compositional differences, while the archaeal fractions were not found to be significantly different. The particle-associated fraction contained more Rhodobacterales and unclassified Myxococcales along with Bacteroidetes, Planctomycetes and chloroplast sequences, whereas the free-living fraction contained more Caulobacterales, Xanthomonadales and Burkholderiales, along with Marine Group A and Gemmatimonadetes. The Eukarya contained a high abundance of Basidiomycota Fungi 18S rRNA genes, as well as representatives from the super-groups Rhizaria, Excavata and Chromalveolata. A diverse clade of diplonemid flagellates was also identified from the eukaryotic phylotypes recovered, which was distinct from previously identified deep-sea pelagic diplonemid groups. The significance of these results to considerations of deep-sea microbial life and particle colonization is discussed in comparison to the few other deep-ocean phylogenetic surveys available.

Seasonal and spatial variation of bacterial community structure in river-mouth areas of Gokasho bay, Japan

This study investigated seasonal and spatial dynamics of the bacterial community in Gokasho bay with denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified 16S rRNA gene fragments. The community structure was related to physico-chemical water conditions in the area examined. The bacterial community clustered into three groups: bacteria collected during January-May; those collected from water at the surface in July and September; and those collected from water at the bottom in July and September and from both depths in November. Canonical correspondence analyses indicated that the seasonal variability in bacterial community was associated with water temperature succession. On the other hand, concentrations of particulate organic matter and nitrite plus nitrate were related to the vertical change in community structure in summer and autumn as well as HNF abundance, suggesting that both top-down and bottom-up control affected the community. The influence of salinity was insignificant though bacterial production was related to salinity. No relationship was observed between the variation in community structure and that in hydrolytic enzyme activity. The results indicate that changes in bacterial activity are not coupled with variation in community structure.

Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing

Bacterial assemblages from subsurface (100 m depth), meso- (200-1000 m depth) and bathy-pelagic (below 1000 m depth) zones at 10 stations along a North Atlantic Ocean transect from 60°N to 5°S were characterized using massively parallel pyrotag sequencing of the V6 region of the 16S rRNA gene (V6 pyrotags). In a dataset of more than 830,000 pyrotags, we identified 10,780 OTUs of which 52% were singletons. The singletons accounted for less than 2% of the OTU abundance, whereas the 100 and 1000 most abundant OTUs represented 80% and 96% respectively of all recovered OTUs. Non-metric Multi-Dimensional Scaling and Canonical Correspondence Analysis of all the OTUs excluding the singletons revealed a clear clustering of the bacterial communities according to the water masses. More than 80% of the 1000 most abundant OTUs corresponded to Proteobacteria of which 55% were Alphaproteobacteria, mostly composed of the SAR11 cluster. Gammaproteobacteria increased with depth and included a relatively large number of OTUs belonging to Alteromonadales and Oceanospirillales. The bathypelagic zone showed higher taxonomic evenness than the overlying waters, albeit bacterial diversity was remarkably variable. Both abundant and low-abundance OTUs were responsible for the distinct bacterial communities characterizing the major deep-water masses. Taken together, our results reveal that deep-water masses act as bio-oceanographic islands for bacterioplankton leading to water mass-specific bacterial communities in the deep waters of the Atlantic.

Are Archaea inherently less diverse than Bacteria in the same environments?

Like Bacteria, Archaea occur in a wide variety of environments, only some of which can be considered 'extreme'. We compare archaeal diversity, as represented by 173 16S rRNA gene libraries described in published reports, to bacterial diversity in 79 libraries from the same source environments. An objective assessment indicated that 114 archaeal libraries and 45 bacterial libraries were large enough to yield stable estimates of total phylotype richness. Archaeal libraries were seldom as large or diverse as bacterial libraries from the same environments. However, a relatively larger proportion of libraries were large enough to effectively capture rare as well as dominant phylotypes in archaeal communities. In contrast to bacterial libraries, the number of phylotypes did not correlate with library size; thus, 'larger' may not necessarily be 'better' for determining diversity in archaeal libraries. Differences in diversity suggest possible differences in ecological roles of Archaea and Bacteria; however, information is lacking on relative abundances and metabolic activities within the sampled communities, as well as the possible existence of microhabitats. The significance of phylogenetic diversity as opposed to functional diversity remains unclear, and should be a high priority for continuing research.