Comparison between MICRO–CARD–FISH and 16S rRNA gene clone libraries to assess the active versus total bacterial community in the coastal Arctic

Dynamics of actively dividing prokaryotes in the western Mediterranean Sea

Microbial community metabolism and functionality play a key role modulating global biogeochemical processes. However, the metabolic activities and contribution of actively growing prokaryotes to ecosystem energy fluxes remain underexplored. Here we describe the temporal and spatial dynamics of active prokaryotes in the different water masses of the Mediterranean Sea using a combination of bromodeoxyuridine labelling and 16S rRNA gene Illumina sequencing. Bulk and actively dividing prokaryotic communities were drastically different and depth stratified. Alteromonadales were rare in bulk communities (contributing 0.1% on average) but dominated the actively dividing community throughout the overall water column (28% on average). Moreover, temporal variability of actively dividing Alteromonadales oligotypes was evinced. SAR86, Actinomarinales and Rhodobacterales contributed on average 3–3.4% each to the bulk and 11, 8.4 and 8.5% to the actively dividing communities in the epipelagic zone, respectively. SAR11 and Nitrosopumilales contributed less to the actively dividing than to the bulk communities during all the study period. Noticeably, the large contribution of these two taxa to the total prokaryotic communities (23% SAR11 and 26% Nitrosopumilales), especially in the meso- and bathypelagic zones, results in important contributions to actively dividing communities (11% SAR11 and 12% Nitrosopumilales). The intense temporal and spatial variability of actively dividing communities revealed in this study strengthen the view of a highly dynamic deep ocean. Our results suggest that some rare or low abundant phylotypes from surface layers down to the deep sea can disproportionally contribute to the activity of the prokaryotic communities, exhibiting a more dynamic response to environmental changes than other abundant phylotypes, emphasizing the role they might have in community metabolism and biogeochemical processes.

Survey of Bacterial Phylogenetic Diversity During the Glacier Melting Season in an Arctic Fjord

To understand bacterial biogeography in response to the hydrographic impact of climate change derived from the Arctic glacier melting, we surveyed bacterial diversity and community composition using bacterial 16S rRNA gene metabarcoding in the seawaters of Kongsfjorden, Svalbard, during summer 2016. In the present study, bacterial biogeography in the Kongsfjorden seawaters showed distinct habitat patterns according to water mass classification and habitat transition between Atlantic and fjord surface waters. Moreover, we estimated phylogenetic diversity of bacterial communities using the net relatedness, nearest taxon, and beta nearest taxon indices. We found the influence of freshwater input from glacier melting in shaping bacterial assemblage composition through the stochastic model. We further evaluated bacterial contributions to phytoplankton-derived dimethylsulfoniopropionate (DMSP) using a quantitative PCR (qPCR) measurement with demethylation (dmdA) and cleavage (dddP) genes of two fundamentally different processes. Our qPCR results imply that bacterial DMSP degradation follows the Atlantic inflow during summer in Kongsfjorden. These findings suggest that the Atlantic inflow and glacial melting influence bacterial community composition and assembly processes and thus affect the degradation of phytoplankton-derived organic matter in an Arctic fjord.

Two different approaches of microbial community structure characterization in riverine epilithic biofilms under multiple stressors conditions: Developing molecular indicators

Microbial communities are major players in the biogeochemical processes and ecosystem functioning of river networks. Despite their importance in the ecosystem, biomonitoring tools relying on prokaryotes are still lacking. Only a few studies have employed both metabarcoding and quantitative techniques such as catalysed reported deposition fluorescence in situ hybridization (CARD-FISH) to analyse prokaryotic communities of epilithic biofilms in river ecosystems. We intended to investigate the efficacy of both techniques in detecting changes in microbial community structure associated with environmental drivers. We report a significant correlation between the prokaryotic community composition and pH in rivers from two different geographical areas in Norway. Both CARD-FISH and metabarcoding data were following the pattern of the environmental variables, but the main feature distinguishing the community composition was the regional difference itself. Beta-dispersion analyses on both CARD-FISH abundance and metabarcoding data revealed higher accuracy of metabarcoding to differentiate regions and river systems. The CARD-FISH results showed high variability, even for samples within the same river, probably due to some unmeasured microscale ecological variability which we could not resolve. We also present a statistical method, which uses variation coefficient and overall prevalence of taxonomic groups, to detect possible biological indicators among prokaryotes using metabarcoding data. The development of new prokaryotic bioindicators would benefit from both techniques used in this study, but metabarcoding seems to be faster and more reliable than CARD-FISH for large scale bio-assessment.

Linking Compositional and Functional Predictions to Decipher the Biogeochemical Significance in DFAA Turnover of Abundant Bacterioplankton Lineages in the North Sea

Deciphering the ecological traits of abundant marine bacteria is a major challenge in marine microbial ecology. In the current study, we linked compositional and functional predictions to elucidate such traits for abundant bacterioplankton lineages in the North Sea. For this purpose, we investigated entire and active bacterioplankton composition along a transect ranging from the German Bight to the northern North Sea by pyrotag sequencing of bacterial 16S rRNA genes and transcripts. Functional profiles were inferred from 16S rRNA data using Tax4Fun. Bacterioplankton communities were dominated by well-known marine lineages including clusters/genera that are affiliated with the Roseobacter group and the Flavobacteria. Variations in community composition and function were significantly explained by measured environmental and microbial properties. Turnover of dissolved free amino acids (DFAA) showed the strongest correlation to community composition and function. We applied multinomial models, which enabled us to identify bacterial lineages involved in DFAA turnover. For instance, the genus Planktomarina was more abundant at higher DFAA turnover rates, suggesting its vital role in amino acid degradation. Functional predictions further indicated that Planktomarina is involved in leucine and isoleucine degradation. Overall, our results provide novel insights into the biogeochemical significance of abundant bacterioplankton lineages in the North Sea.

Diversity of bacterial dimethylsulfoniopropionate degradation genes in surface seawater of Arctic Kongsfjorden

Dimethylsulfoniopropionate (DMSP), which is the major source of organic sulfur in the world's oceans, plays a significant role in the global sulfur cycle. This compound is rapidly degraded by marine bacteria either by cleavage to dimethylsulfide (DMS) or demethylation to 3-methylmercaptopropionate (MMPA). The diversity of genes encoding bacterial demethylation (dmdA) and DMS production (dddL and dddP) were measured in Arctic Kongsfjorden. Both dmdA and dddL genes were detected in all stations along a transect from the outer to the inner fjord, while dddP gene was only found in the outer and middle parts of the fjord. The dmdA gene was completely confined to the Roseobacter clade, while the dddL gene was confined to the genus Sulfitobacter. Although the dddP gene pool was also dominated by homologs from the Roseobacter clade, there were a few dddP genes showing close relationships to both Alphaproteobacter and Gammaproteobacter. The results of this study suggest that the Roseobacter clade may play an important role in DMSP catabolism via both demethylation and cleavage pathways in surface waters of Kongsfjorden during summer.

Bacterial diversity in the South Adriatic Sea during a strong, deep winter convection year

The South Adriatic Sea is the deepest part of the Adriatic Sea and represents a key area for both the Adriatic Sea and the deep eastern Mediterranean. It has a role in dense water formation for the eastern Mediterranean deep circulation cell, and it represents an entry point for water masses originating from the Ionian Sea. The biodiversity and seasonality of bacterial picoplankton before, during, and after deep winter convection in the oligotrophic South Adriatic waters were assessed by combining comparative 16S rRNA sequence analysis and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). The picoplankton communities reached their maximum abundance in the spring euphotic zone when the maximum value of the chlorophyll a in response to deep winter convection was recorded. The communities were dominated by Bacteria, while Archaea were a minor constituent. A seasonality of bacterial richness and diversity was observed, with minimum values occurring during the winter convection and spring postconvection periods and maximum values occurring under summer stratified conditions. The SAR11 clade was the main constituent of the bacterial communities and reached the maximum abundance in the euphotic zone in spring after the convection episode. Cyanobacteria were the second most abundant group, and their abundance strongly depended on the convection event, when minimal cyanobacterial abundance was observed. In spring and autumn, the euphotic zone was characterized by Bacteroidetes and Gammaproteobacteria. Bacteroidetes clades NS2b, NS4, and NS5 and the gammaproteobacterial SAR86 clade were detected to co-occur with phytoplankton blooms. The SAR324, SAR202, and SAR406 clades were present in the deep layer, exhibiting different seasonal variations in abundance. Overall, our data demonstrate that the abundances of particular bacterial clades and the overall bacterial richness and diversity are greatly impacted by strong winter convection.

The bacterial microbiota of Stolotermes ruficeps (Stolotermitidae), a phylogenetically basal termite endemic to New Zealand

Stolotermes ruficeps is a widespread, primitive, lower termite occupying dead and decaying wood of many tree species in New Zealand's temperate forests. We identified core bacterial taxa involved in gut processes through combined DNA- and RNA (cDNA)-based pyrosequencing analysis of the 16S nucleotide sequence from five S. ruficeps colonies. Most family and many genus-level taxa were common to S. ruficeps colonies despite being sampled from different tree species. Major taxa identified were Spirochaetaceae, Elusimicrobiaceae and Porphyromonadaceae. Others less well known in termite guts were Synergistaceae, Desulfobacteraceae, Rhodocyclaceae, Lachnospiraceae and Ruminococcaceae. Synergistaceae, Lachnospiraceae and Spirochaetaceae were well represented in the RNA data set, indicating a high-protein synthesis potential. Using 130,800 sequences from nine S. ruficeps DNA and RNA data sets, we estimated a high level of bacterial richness (4024 phylotypes at 3% genetic distance). Very few abundant phylotypes were site-specific; almost all (95%) abundant phylotypes, representing 97% of data set sequences, were detected in at least two S. ruficeps colonies. This study of a little-researched phylogenetically basal termite identifies core bacteria taxa. These findings will extend inventories of termite gut microbiota and contribute to the understanding of the specificity of termite gut microbiota.

Bacterial community shift is induced by dynamic environmental parameters in a changing coastal ecosystem (northern Adriatic, northeastern Mediterranean Sea)--a 2-year time-series study

The potential link between the microbial dynamics and the environmental parameters was investigated in a semi-enclosed and highly dynamic coastal system (Gulf of Trieste, northern Adriatic Sea, NE Mediterranean Sea). Our comprehensive 2-year time-series study showed that despite the shallowness of this area, there was a significant difference between the surface and the bottom bacterial community structure. The bottom bacterial community was more diverse than the surface one and influenced by sediment re-suspension. The surface seawater temperature had a profound effect on bacterial productivity, while the bacterial community structure was more affected by freshwater-borne nutrients and phytoplankton blooms. Phytoplankton blooms caused an increase of Gammaproteobacteria (Alteromonadaceae, SAR86 and Vibrionaceae) and shift in dominance from SAR11 to Rhodobacteraceae taxon at the surface. Our results propose the importance of the water mass movements as drivers of freshwater-borne nutrients and of allochthonous microbial taxa. This study emphasizes the prediction power based on association networks analyses that are fed with long-term measurements of microbial and environmental parameters. These interaction maps offer valuable insights into the response of marine ecosystem to climate- and anthropogenic-driven stressors.

Uptake of dissolved organic carbon by gammaproteobacterial subgroups in coastal waters of the West Antarctic Peninsula

Heterotrophic bacteria are well known to be key players in the turnover of dissolved organic material (DOM) in the oceans, but the relationship between DOM uptake and bacterial clades is still not well understood. Here we explore the turnover and single-cell use of glucose, an amino acid mixture, N-acetylglucosamine (NAG), and protein by gammaproteobacterial clades in coastal waters of the West Antarctic Peninsula in summer and fall. More than 60% of the cells within two closely related gammaproteobacterial clades, Ant4D3 and Arctic96B-16, were active in using the amino acid mixture, protein, and NAG. In contrast, an average of only 7% of all SAR86 cells used amino acids and protein even in summer when DOM use was high. In addition to DOM uptake within a group, we explored the contribution of the three gammaproteobacterial groups to total community uptake of a compound. SAR86 contributed 5- to 10-fold less than the other gammaproteobacterial subgroups to the uptake of all compounds. We found that the overall contribution of the Ant4D3 clade to DOM uptake was highest, whereas the SAR86 clade contributed the least to DOM turnover in West Antarctic Peninsula waters. Our results suggest that the low growth activity of a bacterial clade leads to low abundance, fewer active cells and a low contribution to the turnover of DOM components.

Selective occurrence of Rhizobiales in frost flowers on the surface of young sea ice near Barrow, Alaska and distribution in the polar marine rare biosphere

Frost flowers are highly saline ice structures that grow on the surface of young sea ice, a spatially extensive environment of increasing importance in the Arctic Ocean. In a previous study, we reported organic components of frost flowers in the form of elevated levels of bacteria and exopolymers relative to underlying ice. Here, DNA was extracted from frost flowers and young sea ice, collected in springtime from a frozen lead offshore of Barrow, Alaska, to identify bacteria in these understudied environments. Evaluation of the distribution of 16S rRNA genes via four methods (microarray analysis, T-RFLP, clone library and shotgun metagenomic sequencing) indicated distinctive bacterial assemblages between the two environments, with frost flowers appearing to select for Rhizobiales. A phylogenetic placement approach, used to evaluate the distribution of similar Rhizobiales sequences in other polar marine studies, indicated that some of the observed strains represent widely distributed members of the marine rare biosphere in both the Arctic and Antarctic.

Spatial patterns of bacterial and archaeal communities along the Romanche Fracture Zone (tropical Atlantic)

The composition of prokaryotic communities was determined in the meso- and bathypelagic waters funneled through the Romanche Fracture Zone (RFZ, 2°7′S, 31°79′W to 0°6′N, 14°33′W) in the tropical Atlantic. Distinct water masses were identified based on their physical and chemical characteristics. The bacterial and archaeal communities were depth-stratified with a total of 116 and 25 operational taxonomic units (OTUs), respectively, distributed among the distinct water masses as revealed by terminal restriction fragment length polymorphism, and cloning and sequencing. The relative abundance of Thaumarchaeota, determined by catalyzed reporter deposition-fluorescence in situ hybridization, was significantly higher in deeper layers (Antarctic Bottom Water, AABW, > 4000 m depth), contributing up to 31% to the total prokaryotic community, than in the mesopelagic and lower euphotic layer. Although the contribution of SAR11 to bacterial abundance did not increase with depth, SAR202, SAR324, SAR406 and Alteromonas did increase with depth. Terminal restriction fragment length polymorphism analysis revealed successional changes in the bacterial and archaeal community composition of the North Atlantic Deep Water (NADW) with a passage time through the RFZ of c. 4 months but not in the under- and overlying water masses. Our results indicate that specific water masses harbor distinct bacterial and archaeal communities and that the prokaryotic community of the NADW undergoes successional changes in this conduit between the western and eastern Atlantic basin. Apparently, in the absence of major input of organic matter to specific deep-water masses, the indigenous prokaryotic community adapts to subtle physical and biogeochemical changes in the water mass within a time frame of weeks, similar to the reported seasonal changes in surface water prokaryotic communities.

Bacterioplankton community structure in the Arctic waters as revealed by pyrosequencing of 16S rRNA genes

Fjords and open oceans are two typical marine ecosystems in the Arctic region, where glacial meltwater and sea ice meltwater have great effects on the bacterioplankton community structure during the summer season. This study aimed to determine the differences in bacterioplankton communities between these two ecosystems in the Arctic region. We conducted a detailed census of microbial communities in Kongsfjorden (Spitsbergen) and the Chukchi Borderland using high-throughput pyrosequencing of the 16S rRNA gene. Gammaproteobacteria and Bacteroidetes were the dominant members of the bacterioplankton community in Kongsfjorden. By contrast, the most abundant bacterial groups in the surface seawater samples from the Chukchi Borderland were Alphaproteobacteria and Actinobacteria. Differences in bacterial communities were found between the surface and subsurface waters in the investigation area of the Chukchi Borderland, and significant differences in bacterial community structure were also observed in the subsurface water between the shelf and deep basin areas. These results suggest the effect of hydrogeographic conditions on bacterial communities. Ubiquitous phylotypes found in all the investigated samples belonged to a few bacterial groups that dominate marine bacterioplankton communities. The sequence data suggested that changes in environmental conditions result in abundant rare phylotypes and reduced amounts of other phylotypes.