Controls on planktonic foraminifera apparent calcification depths for the northern equatorial Indian Ocean

Within the world’s oceans, regionally distinct ecological niches develop due to differences in water temperature, nutrients, food availability, predation and light intensity. This results in differences in the vertical dispersion of planktonic foraminifera on the global scale. Understanding the controls on these modern-day distributions is important when using these organisms for paleoceanographic reconstructions. As such, this study constrains modern depth habitats for the northern equatorial Indian Ocean, for 14 planktonic foraminiferal species (G. ruber, G. elongatus, G. pyramidalis, G. rubescens, T. sacculifer, G. siphonifera, G. glutinata, N. dutertrei, G. bulloides, G. ungulata, P. obliquiloculata, G. menardii, G. hexagonus, G. scitula) using stable isotopic signatures (δ¹⁸O and δ¹³C) and Mg/Ca ratios. We evaluate two aspects of inferred depth habitats: (1) the significance of the apparent calcification depth (ACD) calculation method/equations and (2) regional species-specific ACD controls. Through a comparison with five global, (sub)tropical studies we found the choice of applied equation and δ¹⁸O_sw significant and an important consideration when comparing with the published literature. The ACDs of the surface mixed layer and thermocline species show a tight clustering between 73–109 m water depth coinciding with the deep chlorophyll maximum (DCM). Furthermore, the ACDs for the sub-thermocline species are positioned relative to secondary peaks in the local primary production. We surmise that food source plays a key role in the relative living depths for the majority of the investigated planktonic foraminifera within this oligotrophic environment of the Maldives and elsewhere in the tropical oceans.

Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow Sea

The Yellow Sea features unique characteristics due to strong tides and nutrient-enriched freshwater outflows from China and Korea. The coupling of archaeal and bacterial assemblages associated with environmental factors at two bay areas in the Yellow Sea was investigated. Temporal variations of the archaeal and bacterial assemblages were shown to be greater than the spatial variations based on an analysis of the 16S rRNA gene sequences. Distinct temporal dynamics of both planktonic archaeal and bacterial assemblages was associated with temperature, NO₂^-, and chlorophyll a ([chl-a]) concentrations in the bays of the Yellow Sea. The [chl-a] was the prime predictor of bacterial abundance, and some taxa were clearly correlated with [chl-a]. Bacteroidetes and Alpha-proteobacteria dominated at high [chl-a] stations while Gamma-proteobacteria (esp. SAR86 clade) and Actinobacteria (Candidatus Actinomarina clade) were abundant at low [chl-a] stations. The archaeal abundance was comparable with the bacterial abundance in most of the October samples. Co-dominance of Marine Group II (MGII) and Candidatus Nitrosopumilus suggests that the assimilation of organic nitrogen by MGII could be coupled with nitrification by ammonia-oxidizing archaea. The distinct temporal dynamics of the archaeal and bacterial assemblages might be attributable to the strong tides and the inflow of nutrient-rich freshwater.

Environmental conditions and neutral processes shape the skin microbiome of European catfish (Silurus glanis) populations of Southwestern France

Teleost fishes interact with diverse microbial communities, playing crucial functions for host fitness. While gut microbiome has been extensively studied, skin microbiome has been overlooked. Specifically, there is no assessment of the relative impact of host and environmental factors on microbiome variability as well as neutral processes shaping fish skin microbiome. Here, we assessed the skin microbiome of a Siluriforme, the European catfish (Silurus glanis) sampled in four sites located in Southwestern France. We assessed the relative roles of individual features (body size and genetic background), local environment and neutral processes in shaping skin microbiome. Catfish skin microbiome composition was distinct to that of other freshwater fish species previously studied with high abundances of Gammaproteobacteria and Bacteroidetes. We found no effect of catfish individual genotype and body size on the structure of its associated skin microbiome. Geographical location was the best catfish skin microbiome structure predictor, together with neutral models of microbiome assembly.

Microbial eukaryotes in the suboxic chemosynthetic ecosystem of Movile Cave, Romania

Movile Cave is a small system of partially inundated galleries in limestone settings close to the Black Sea in Southeast Romania. Isolated from the surface for 6 million years, its sulfidic, methane and ammonia-rich waters harbour unique chemosynthetic prokaryotic communities that include sulphur and ammonium-metabolizing chemolithotrophs, methanogens, methanotrophs and methylotrophs. The cave also harbours cave-dwelling invertebrates and fungi, but the diversity of other microbial eukaryotes remained completely unknown. Here, we apply an 18S rRNA gene-based metabarcoding approach to study the composition of protist communities in floating microbial mats and plankton from a well-preserved oxygen-depleted cave chamber. Our results reveal a wide protist diversity with, as dominant groups, ciliates (Alveolata), Stramenopiles, especially bicosoecids, and jakobids (Excavata). Ciliate sequences dominated both, microbial mats and plankton, followed by either Stramenopiles or excavates. Stramenopiles were more prominent in microbial mats, whereas jakobids dominated the plankton fraction of the oxygen-depleted water column. Mats cultured in the laboratory were enriched in Cercozoa. Consistent with local low oxygen levels, Movile Cave protists are most likely anaerobic or microaerophilic. Several newly detected OTU clades were very divergent from cultured species or environmental sequences in databases and represent phylogenetic novelty, notably within jakobids. Movile Cave protists likely cover a variety of ecological roles in this ecosystem including predation, parasitism, saprotrophy and possibly diverse prokaryote-protist syntrophies.

Culture dependent and independent analysis and appraisal of early stage biofilm-forming bacterial community composition in the Southern coastal seawater of India

Microbial aggregation on artificial surfaces is a fundamental phenomenon in aquatic systems that lead to biofouling, corrosion and influence the buoyancy of plastic materials. Despite the maritime activities and with nearshore large industrial sector, Laccadive Sea in the Indian Ocean has rarely been investigated for characterizing early biofilm-forming bacterial community. The present investigation was aimed to catalogue the primary colonizers on artificial surfaces and their comparison with planktonic community in southern coastal seawater of India. Surface seawater samples and biofilm assembled on three artificial surfaces over a period of 72 h of immersion in the intake area of a nuclear power plant at Kudankulam, India were collected. The structure of surface assemblages and plankton were unveiled by employing culture dependent, DGGE and NGS methods. In static condition, a collection of aerobic heterotrophic bacteria was screened in vitro for their ability to form potent biofilm. Proteobacteria preponderated the communities both in seawater and natural biofilm and Gammaproteobacteria accounted for >85% in the latter. Vibrionaceae, Alteromonadaceae and Pseudoalteromonadaceae dominated the biofilm community and constituted for 41, 25 and 8%, respectively. In contrast to other studies that showed Rhodobacteraceae family of Alphaproteobacteria as predominant component, we found Vibrionaceae of Gammaproteobacteria as dominant group in early stage of biofilm formation. Both DGGE and NGS data indicated that the attached community is noticeably distinct from those suspended in water column and form the basis for the proposed hypothesis of species sorting theory, that is, the local environmental conditions influence bacterial community assembly. Collectively, the data are testament for species sorting process that occur during initial assembly of bacterial community in marine environment and shed light on the structure of marine bacterial biofilm development. The outcome of the present study is of immense importance for designing long-term, efficient and appropriate strategies to control the biofouling phenomenon.

Unassigned diversity of planktonic foraminifera from environmental sequencing revealed as known but neglected species

Most research on extant planktonic foraminifera has been directed towards larger species (>0.150 mm) which can be easily manipulated, counted and yield enough calcite for geochemical analyses. This has drawn attention towards the macroperforate clade and created an impression of their numerical and ecological dominance. Drawing such conclusions from the study of such “giants” is a dangerous path. There were times in the evolutionary history of planktonic foraminifera when all species were smaller than 0.1 mm and indeed numerous small taxa, mainly from the microperforate clade, have been formally described from the modern plankton. The significance of these small, obscure and neglected species is poorly characterized and their relationship to the newly discovered hyperabundant but uncharacterized lineages of planktonic foraminifera in metabarcoding datasets is unknown. To determine, who is hiding in the metabarcoding datasets, we carried out an extensive sequencing of 18S rDNA targeted at small and obscure species. The sequences of the newly characterized small and obscure taxa match many of the previously uncharacterized lineages found in metabarcoding data. This indicates that most of the modern diversity in planktonic foraminifera has been taxonomically captured, but the role of the small and neglected taxa has been severely underestimated.

Stratification, nitrogen fixation, and cyanobacterial bloom stage regulate the planktonic food web structure

Changes in the complexity of planktonic food webs may be expected in future aquatic systems due to increases in sea surface temperature and an enhanced stratification of the water column. Under these conditions, the growth of unpalatable, filamentous, N₂ -fixing cyanobacterial blooms, and their effect on planktonic food webs will become increasingly important. The planktonic food web structure in aquatic ecosystems at times of filamentous cyanobacterial blooms is currently unresolved, with discordant lines of evidence suggesting that herbivores dominate the mesozooplankton or that mesozooplankton organisms are mainly carnivorous. Here, we use a set of proxies derived from amino acid nitrogen stable isotopes from two mesozooplankton size fractions to identify changes in the nitrogen source and the planktonic food web structure across different microplankton communities. A transition from herbivory to carnivory in mesozooplankton between more eutrophic, near-coastal sites and more oligotrophic, offshore sites was accompanied by an increasing diversity of microplankton communities with aging filamentous cyanobacterial blooms. Our analyses of 124 biotic and abiotic variables using multivariate statistics confirmed salinity as a major driver for the biomass distribution of non-N₂ -fixing microplankton species such as dinoflagellates. However, we provide strong evidence that stratification, N₂ fixation, and the stage of the cyanobacterial blooms regulated much of the microplankton diversity and the mean trophic position and size of the metabolic nitrogen pool in mesozooplankton. Our empirical, macroscale data set consistently unifies contrasting results of the dominant feeding mode in mesozooplankton during blooms of unpalatable, filamentous, N₂ -fixing cyanobacteria by identifying the at times important role of heterotrophic microbial food webs. Thus, carnivory, rather than herbivory, dominates in mesozooplankton during aging and decaying cyanobacterial blooms with hitherto uncharacterized consequences for the biogeochemical functions of mesozooplankton.

The Impact of Anthropogenic Disturbance on Bacterioplankton Communities During the Construction of Donghu Tunnel (Wuhan, China)

Bacterioplankton are both primary producers and primary consumers in aquatic ecosystems, which were commonly investigated to reflect environmental changes, evaluate primary productivity, and assess biogeochemical cycles. However, there is relatively less understanding of their responses to anthropogenic disturbances such as constructions of dams/tunnels/roads that may significantly affect the aquatic ecosystem. To fill such gap, this study focused on the bacterioplankton communities' diversity and turnover during a tunnel construction across an urban lake (Lake Donghu, Wuhan, China), and five batches of samples were collected within 2 months according to the tunnel construction progress. Results indicated that both resources and predator factors contributed significant to the variations of bacterioplankton communities, but the closed area and open areas showed different diversity patterns due to the impacts of tunnel construction. Briefly, the phytoplankton, TN, and TP in water were still significantly correlated with the bacterioplankton composition and diversity like that in normal conditions. Additionally, the organic matter, TN, and NH₄-N in sediments also showed clear effects on the bacterioplankton. However, the predator effects on the bacterioplankton in the closed-off construction area mainly derived from large zooplankton (i.e., cladocerans), while small zooplankton such as protozoa and rotifers are only responsible for weak predator effects on the bacterioplankton in the open areas. Further analysis about the ecological driving forces indicated that the bacterioplankton communities' turnover during the tunnel construction was mainly governed by the homogeneous selection due to similar environments within the closed area or the open areas at two different stages. This finding suggests that bacterioplankton communities can quickly adapt to the environmental modifications resulting from tunnel construction activities. This study can also give references to enhance our understanding on bacterioplankton communities' response to ecological and environmental changes due to intensification of construction and urbanization in and around lake ecosystems.

Annotated 18S and 28S rDNA reference sequences of taxa in the planktonic diatom family Chaetocerotaceae

The species-rich diatom family Chaetocerotaceae is common in the coastal marine phytoplankton worldwide where it is responsible for a substantial part of the primary production. Despite its relevance for the global cycling of carbon and silica, many species are still described only morphologically, and numerous specimens do not fit any described taxa. Nowadays, studies to assess plankton biodiversity deploy high throughput sequencing metabarcoding of the 18S rDNA V4 region, but to translate the gathered metabarcodes into biologically meaningful taxa, there is a need for reference barcodes. However, 18S reference barcodes for this important family are still relatively scarce. We provide 18S rDNA and partial 28S rDNA reference sequences of 443 morphologically characterized chaetocerotacean strains. We gathered 164 of the 216 18S sequences and 244 of the 413 28S sequences of strains from the Gulf of Naples, Atlantic France, and Chile. Inferred phylogenies showed 84 terminal taxa in seven principal clades. Two of these clades included terminal taxa whose rDNA sequences contained spliceosomal and Group IC1 introns. Regarding the commonly used metabarcode markers in planktonic diversity studies, all terminal taxa can be discriminated with the 18S V4 hypervariable region; its primers fit their targets in all but two species, and the V4-tree topology is similar to that of the 18S. Hence V4-metabarcodes of unknown Chaetocerotaceae are assignable to the family. Regarding the V9 hypervariable region, most terminal taxa can be discriminated, but several contain introns in their primer targets. Moreover, poor phylogenetic resolution of the V9 region affects placement of metabarcodes of putative but unknown chaetocerotacean taxa, and hence, uncertainty in taxonomic assignment, even of higher taxa.

Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments

Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.

Plankton community assessment in anthropogenic-impacted oligotrophic coastal regions

Microbial planktonic communities are critical components of marine biogeochemical pathways. Despite this, there is still limited knowledge on the dynamics of this group in warm and oligotrophic waters. We used high-throughput sequencing to characterise the bacterial (16S rRNA) and eukaryotic (18S rRNA) microbial plankton communities in two regions under the influence of anthropogenic impacts (a port and sewage outflow) and a coastal region with no direct anthropogenic disturbances in the central Red Sea. Overall, bacterial and eukaryotic components responded in a similar way to the environmental conditions. Community composition and structure were more sensitive than alpha diversity measures to environmental impacts. With the exception of eukaryotes, for which the number of OTU differed significantly between sampling periods in all the regions, environmental changes associated with anthropogenic pressures seem to be better reflected by variations in the relative dominance of microbial groups. For example, elevated proportional abundances of nitrifying and sewage-/faecal-related bacteria at the impacted sites were observed compared with the coastal region. The recently developed microgAMBI also appeared to correlate well with the level of anthropogenic impact the regions experienced, showing the potential to be applied in oligotrophic waters.

Future-proofing the Cenozoic macroperforate planktonic foraminifera phylogeny of Aze & others (2011)

The unique macroevolutionary dataset of Aze & others has been transferred onto the TimeScale Creator visualisation platform while, as much as practicable, preserving the original unrevised content of its morphospecies and lineage evolutionary trees. This is a "Corrected Version" (not a revision), which can serve as an on-going historical case example because it is now updatable with future time scales. Both macroevolutionary and biostratigraphic communities are now equipped with an enduring phylogenetic database of Cenozoic macroperforate planktonic foraminiferal morphospecies and lineages for which both graphics and content can be visualised together. Key to maintaining the currency of the trees has been specification of time scales for sources of stratigraphic ranges; these scales then locate the range dates within the calibration series. Some ranges or their sources have undergone mostly minor corrections or amendments. Links between lineage and morphospecies trees have been introduced to improve consistency and transparency in timing within the trees. Also, Aze & others' dual employment of morphospecies and lineage concepts is further elaborated here, given misunderstandings that have ensued. Features displayed on the trees include options for line styles for additional categories for range extensions or degrees of support for ancestor-descendant proposals; these have been applied to a small number of instances as an encouragement to capture more nuanced data in the future. In addition to labeling of eco- and morpho-groups on both trees, genus labels can be attached to the morphospecies tree to warn of polyphyletic morphogenera, and the lineage codes have been decoded to ease their recognition. However, it is the mouse-over pop-ups that provide the greatest opportunity to embed supporting information in the trees. They include details for stratigraphic ranges and their recalibration steps, positions relative to the standard planktonic-foraminiferal zonation, and applications as datums, as well as mutual listings between morphospecies and lineages which ease the tracing of their interrelated contents. The elaboration of the original dataset has been captured in a relational database, which can be considered a resource in itself, and, through queries and programming, serves to generate the TimeScale Creator datapacks.

Microplankton dynamics of a coastal lagoon, Chilika: interactive effect of environmental parameters on microplankton groups

Microplankton population of Asia's largest coastal lagoon Chilika was studied for five major groups, bacillariophyceae, cyanophyceae, chlorophyceae, dinophyceae, rotifera, and tintinninae. The study reported presence of 233 species of microplankton whose average annual abundance was 1631 cells/l. The physicochemical parameters contributing to the spatio-temporal fluctuations in microplankton diversity, abundance, and community structure were identified as salinity, pH, DO, nitrate, and silicate. Salinity, transparency, depth, and silicate most explained the abundance of bacillariophyceae; nitrate, pH, and DO influenced cyanophyceae; salinity, transparency, and chlorophyll concentration influenced chlorophyceae; salinity, depth, and water temperature influenced dinophyceae; salinity, free CO2, and nitrate-influenced rotifers, whereas salinity, pH, DO, and depth influenced tintinnids. Biotic-abiotic relationships revealed particular preference of environmental conditions at species level in groups like bacillariophyceae, cyanophyceae, and dinophyceae. Although the lagoon is shallow, bacillariophyceae-environment interaction showed depth can be a critical factor for species like Aulocoseira sp., Amphipleura sp., and Rhophalodia sp. Species of dinoflagellates like Dinophysis caudata, Noctiluca scintillans, and Protoperidinium proliferated in lower level of silicate. Unlike other cyanophyceae species Streptococcus sp., Chroococcus sp., Diplococcus sp., Aphanocapsa sp., and Gloeocapsa sp. were negatively influenced by nitrate concentration. The study provides better scope for ecological management of the lagoon with respect to conserving biodiversity and hydrological quality of the ecosystem.

Hidden in plain sight-highly abundant and diverse planktonic freshwater Chloroflexi

BACKGROUND

Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total prokaryotes), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwater Chloroflexi community is largely unknown except for a single metagenome-assembled genome of CL500-11.

RESULTS

Here, we provide the first extensive examination of the community composition of this cosmopolitan phylum in a range of pelagic habitats (176 datasets) and highlight the impact of salinity and depth on their phylogenomic composition. Reconstructed genomes (53 in total) provide a perspective on the phylogeny, metabolism, and distribution of three novel classes and two family-level taxa within the phylum Chloroflexi. We unraveled a remarkable genomic diversity of pelagic freshwater Chloroflexi representatives that thrive not only in the hypolimnion as previously suspected, but also in the epilimnion. Our results suggest that the lake hypolimnion provides a globally stable habitat reflected in lower species diversity among hypolimnion-specific CL500-11 and TK10 clusters in distantly related lakes compared to a higher species diversity of the epilimnion-specific SL56 cluster. Cell volume analyses show that the CL500-11 are among the largest prokaryotic cells in the water column of deep lakes and with a biomass to abundance ratio of two they significantly contribute to the deep lake carbon flow. Metabolic insights indicate participation of JG30-KF-CM66 representatives in the global cobalamin production via cobinamide to cobalamin salvage pathway.

CONCLUSIONS

Extending phylogenomic comparisons to brackish and marine habitats suggests salinity as the major influencer of the community composition of the deep-dwelling Chloroflexi in marine (SAR202) and freshwater (CL500-11) habitats as both counterparts thrive in intermediate brackish salinity; however, freshwater habitats harbor the most phylogenetically diverse community of pelagic Chloroflexi representatives that reside both in epi- and hypolimnion.

Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling

Short timescale observations are valuable for understanding microbial ecological processes. We assessed dynamics in relative abundance and potential activities by sequencing the small sub-unit ribosomal RNA gene (rRNA gene) and rRNA molecules (rRNA) of Bacteria, Archaea, and Eukaryota once to twice daily between March 2014 and May 2014 from the surface ocean off Catalina Island, California. Typically Ostreococcus, Braarudosphaera, Teleaulax, and Synechococcus dominated phytoplankton sequences (including chloroplasts) while SAR11, Sulfitobacter, and Fluviicola dominated non-phytoplankton Bacteria and Archaea. We observed short-lived increases of diatoms, mostly Pseudo-nitzschia and Chaetoceros, with quickly responding Bacteria and Archaea including Flavobacteriaceae (Polaribacter & Formosa), Roseovarius, and Euryarchaeota (MGII), notably the exact amplicon sequence variants we observed responding similarly to another diatom bloom nearby, 3 years prior. We observed correlations representing known interactions among abundant phytoplankton rRNA sequences, demonstrating the biogeochemical and ecological relevance of such interactions: (1) The kleptochloroplastidic ciliate Mesodinium 18S rRNA gene sequences and a single Teleaulax taxon (via 16S rRNA gene sequences) were correlated (Spearman r = 0.83) yet uncorrelated to a Teleaulax 18S rRNA gene OTU, or any other taxon (consistent with a kleptochloroplastidic or karyokleptic relationship) and (2) the photosynthetic prymnesiophyte Braarudosphaera bigelowii and two strains of diazotrophic cyanobacterium UCYN-A were correlated and each taxon was also correlated to other taxa, including B. bigelowii to a verrucomicrobium and a dictyochophyte phytoplankter (all r > 0.8). We also report strong correlations (r > 0.7) between various ciliates, bacteria, and phytoplankton, suggesting interactions via currently unknown mechanisms. These data reiterate the utility of high-frequency time series to show rapid microbial reactions to stimuli, and provide new information about in situ dynamics of previously recognized and hypothesized interactions.

Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes

Unraveling the relative importance of ecological processes regulating microbial community structure is a central goal in microbial ecology. Here, we used high-throughput sequencing to examine the relative contribution of selective and neutral processes in the assembly of abundant and rare subcommunities from three subtropical bays of China. We found that abundant and rare bacterial taxa were distinctly different in diversity, despite the similar biogeographic patterns and strong distance-decay relationships, but the dispersal of rare bacterial taxa was more limited than that of abundant taxa. Furthermore, the environmental (selective processes) and spatial (neutral processes) factors seemed to govern the assembly and biogeography of abundant and rare bacterial subcommunities, although both factors explained only a small fraction of variation within the rare subcommunity. More importantly, variation partitioning (based on adjusted R2 in redundancy analysis) showed that spatial factors exhibited a slightly greater influence on both abundant and rare subcommunities compared to environmental selection; however, the abundant subcommunity had a much stronger response to spatial factors (17.3% of pure variance was explained) than that shown by the rare bacteria (3.5%). These results demonstrate that environmental selection and neutral processes explained the similar biogeographic patterns of abundant and rare subcommunities, but a large proportion of unexplained variation in the rare taxa (91.1%) implies that more complex assembly mechanisms may exist to shape the rare bacterial assemblages in the three subtropical bays.

Repeated disturbances affect functional but not compositional resistance and resilience in an aquatic bacterioplankton community

Disturbances are believed to be one of the main factors influencing variations in community diversity and functioning. Here we investigated if exposure to a pH press disturbance affected the composition and functional performance of a bacterial community and its resistance, recovery and resilience to a second press disturbance (salt addition). Lake bacterial assemblages were initially exposed to reduced pH in six mesocosms whereas another six mesocosms were kept as reference. Seven days after the pH disturbance, three tanks from each treatment were exposed to a salt disturbance. Both bacterial production and enzyme activity were negatively affected by the salt treatment, regardless if the communities had been subject to a previous disturbance or not. However, cell-specific enzyme activity had a higher resistance in communities pre-exposed to the pH disturbance compared to the reference treatment. In contrast, for cell-specific bacterial production resistance was not affected, but recovery was faster in the communities that had previously been exposed to the pH disturbance. Over time, bacterial community composition diverged among treatments, in response to both pH and salinity. The difference in functional recovery, resilience and resistance may depend on differences in community composition caused by the pH disturbance, niche breadth or acquired stress resistance.

Taxonomical Resolution and Distribution of Bacterioplankton Along the Vertical Gradient Reveals Pronounced Spatiotemporal Patterns in Contrasted Temperate Freshwater Lakes

We examined the relationship between viruses and co-occurring bacterial communities across spatiotemporal scale in two contrasting freshwater lakes, namely meromictic Lake Pavin and dimictic Lake Aydat (Central France). Next-generation sequencing of 16S rRNA genes suggested distinct patterns in bacterioplankton community composition (BCC) between the lakes over depths and seasons. BCC were generally dominated by members of Actinobacteria, Proteobacteria, and Bacteroidetes covering about 95% of all sequences. Oxygen depletion at the bottom waters in Aydat and existence of permanent anoxia in the monimolimnion of Pavin resulted in the occurrence and dominance of lesser known members of lake communities such as Methylotenera, Methylobacter, Gallionella, Sulfurimonas, and Syntrophus in Pavin and Methylotenera and Sulfuritalea in Aydat. Differences in BCC appeared strongly related to dissolved oxygen concentration, temperature, viral infection, and virus-to-bacteria ratio. UniFrac analysis indicated a clear distinction in BCC when the percentage of viral infected bacterial cells and virus-to-bacteria ratio exceeded a threshold level of 10% and 5, respectively, suggesting a link between viruses and their potential bacterial host communities. Our study revealed that in both the lakes, the prevailing environmental factors across time and space structured and influenced the adaptation of bacterial communities to specific ecological niches.

Community assembly processes underlying phytoplankton and bacterioplankton across a hydrologic change in a human-impacted river

Although the influence of microbial community assembly processes on aquatic ecosystem function and biodiversity is well known, the processes that govern planktonic communities in human-impacted rivers remain largely unstudied. Here, we used multivariate statistics and a null model approach to test the hypothesis that environmental conditions and obstructed dispersal opportunities, dictate a deterministic community assembly for phytoplankton and bacterioplankton across contrasting hydrographic conditions in a subtropical mid-sized river (Jiulong River, southeast China). Variation partitioning analysis showed that the explanatory power of local environmental variables was larger than that of the spatial variables for both plankton communities during the dry season. During the wet season, phytoplankton community variation was mainly explained by local environmental variables, whereas the variance in bacterioplankton was explained by both environmental and spatial predictors. The null model based on Raup-Crick coefficients for both planktonic groups suggested little evidences of the stochastic processes involving dispersal and random distribution. Our results showed that hydrological change and landscape structure act together to cause divergence in communities along the river channel, thereby dictating a deterministic assembly and that selection exceeds dispersal limitation during the dry season. Therefore, to protect the ecological integrity of human-impacted rivers, watershed managers should not only consider local environmental conditions but also dispersal routes to account for the effect of regional species pool on local communities.

Distinctive Patterns in the Taxonomical Resolution of Bacterioplankton in the Sediment and Pore Waters of Contrasted Freshwater Lakes

Bacteria assemblages in lake sediments play a key role in various biogeochemical processes, yet their association with interstitial pore waters has been scarcely investigated. In this study, we utilized Illumina next-generation amplicon sequencing of the 16S rRNA gene to characterize the seasonal bacterial communities in the sediments and pore waters of three contrasted temperate freshwater lakes, namely Pavin, Aydat, and Grangent (French Massif Central). Despite occupying seemingly similar habitats, bacterial communities differed substantially between sediments and pore waters at all seasons with low sharing of operational taxonomic units (OTUs, 6.7 to 20.3%) between them. Sediment-associated bacteria were more rich and diverse than pore water bacteria, indicating a high heterogeneity in the sediment microhabitat. The changes in both sediment and pore water bacterial communities were lake and season specific. The bacterial community showed distinct differences between the lakes, with larger presence of strict anaerobes such as Syntrophus, Syntrophorhabdus, and Sulfuricurvum in the pore water and sediments of Pavin responsible for carbon and sulfur cycling. In both Aydat and Grangent, the hgcI_clade dominated throughout the study period in the pore waters. The higher representation of lesser-known transient members of lake communities such as Methylotenera in the pore waters of Aydat, and Clostridium and Sulfuricurvum in the pore and sediments of Grangent, respectively, were observed during the period of temporary anoxia in summer caused by lake stratification. Our study revealed that in the investigated lakes, the prevailing environmental factors across time and space structured and influenced the adaptation of bacterial communities to specific ecological niches.

Community Composition and Diversity of Coastal Bacterioplankton Assemblages in Lakes Michigan, Erie, and Huron

The Laurentian Great Lakes, including Lakes Superior, Michigan, Huron, Erie, and Ontario, located in the eastern part of North America are considered the largest of freshwater lakes in the world; however, very little is known about the diversity and distribution of indigenous microbial assemblages within these vast bodies of freshwater systems. Therefore, to delineate the microbial structure and community composition in these aquatic environments, combinations of high-throughput sequencing and fluorescent in situ hybridization (FISH) approaches were utilized to quantitatively characterize the occurrence, diversity, and distribution of bacterioplankton assemblages in six different sites located along the coastal regions of Lakes Michigan, Huron, and Erie. Phylogenetic examination showed a diverse bacterial community belonging to 11 different taxonomic groups. Pyrosequencing results revealed that the majority of the sequences were clustered into four main groups, i.e., Proteobacteria, Bacteriodetes, Actinobacteria, and Cyanobacteria, while fluorescent in situ hybridization also showed the numerical dominance of members of the Gammaproteobacteria and the Cytophaga-Flavobacterium in the six lake sites examined. Overall, the assemblages were shown to be quite diverse in distribution among the lake sites examined, comprising mostly of various heterotrophic populations, with the exception of the Lake Erie-Sandusky Bay site with more than 50% domination by autotrophic Cyanobacteria. This indicates that combinations of factors including water chemistry and various anthropogenic disturbances as well as the lake morphometric characteristics are probably influencing the community structure and diversity of the bacterial assemblages within the systems.

Are oceanic fronts ecotones? Seasonal changes along the subtropical front show fronts as bacterioplankton transition zones but not diversity hotspots

Ecotones are regarded as diversity hotspots in terrestrial systems, but it is unknown if this 'ecotone effect' occurs in the marine environment. Oceanic fronts are widespread mesoscale features, present in the boundary between different water masses, and are arguably the best potential examples of ecotones in the ocean. Here we performed the first seasonal study along an oceanic front, combining 16S rRNA gene sequencing coupled with a high spatial resolution analysis of the physical properties of the water masses. Using the Subtropical Frontal Zone off New Zealand we demonstrate that fronts delimit shifts in bacterioplankton community composition between water masses, but that the strength of this effect is seasonally dependent. While creating a transition zone where physicochemical parameters and bacterioplankton communities get mixed, this ecotone does not result in increased diversity. Thus unlike terrestrial ecotones, oceanic fronts are boundaries but not hotspots of bacterioplankton diversity in the ocean.

A comparative study of prokaryotic diversity and physicochemical characteristics of Devils Hole and the Ash Meadows Fish Conservation Facility, a constructed analog

Devils Hole is the sole natural habitat of the critically endangered Devils Hole pupfish (Cyprinodon diabolis). To establish a backup population, the Ash Meadows Fish Conservation Facility (AMFCF), a full-scale replica of the uppermost 6.7 m of Devils Hole, was constructed by management agencies in the mid-2010s. Despite rigorous efforts to mimic the bathymetric and physical details of the Devils Hole environment, the biogeochemistry and microbiology of the AMFCF refuge tank remain largely unaddressed. We evaluated water physicochemistry and employed Illumina DNA sequencing of 16S rRNA gene libraries to evaluate planktonic and benthic bacterial and archaeal community composition within their respective physicochemical contexts in Devils Hole and AMFCF on the same day. Major ion concentrations were consistent between the two systems, but water temperature and dissolved oxygen dynamics differed. Bioavailable nitrogen (primarily nitrate) was 5x lower in AMFCF. Devils Hole and AMFCF nitrogen:phosphorus molar ratios were 107:1 and 22:1, indicative of different nutrient control mechanisms. Both sites are microbiologically diverse, with over 40 prokaryotic phyla represented at each, with 37 shared between them and nearly than half deriving from candidate divisions. The abundance and composition of predicted photosynthetic primary producers (Cyanobacteria) was markedly different between sites: Devils Hole planktonic and sediment communities were dominated by Oscillatoria spp. (13.2% mean relative abundance), which proved virtually undetectable in AMFCF. Conversely, AMFCF was dominated by a predicted heterotroph from the Verrucomicrobiaceae family (31.7%); which was comparatively rare (<2.4%) in Devils Hole. We propose that the paucity of bioavailable nitrogen in AMFCF, perhaps resulting from physical isolation from allochthonous environmental inputs, is reflected in the microbial assemblage disparity, influences biogeochemical cycling of other dissolved constituents, and may ultimately impact survivorship and recruitment of refuge populations of the Devils Hole pupfish.

Salinity Drives the Virioplankton Abundance but Not Production in Tropical Coastal Lagoons

Viruses are the most abundant components of microbial food webs and play important ecological and biogeochemical roles in aquatic ecosystems. Virioplankton is regulated by several environmental factors, such as salinity, turbidity, and humic substances. However, most of the studies aimed to investigate virioplankton regulation were conducted in temperate systems combining a limited range of environmental variables. In this study, virus abundance and production were determined and their relation to bacterial and limnological variables was assessed in 20 neighboring shallow tropical coastal lagoons that present wide environmental gradients of turbidity (2.32-571 NTU), water color (1.82-92.49 m^-1), dissolved organic carbon (0.71-16.7 mM), salinity (0.13-332.1‰), and chlorophyll-a (0.28 to 134.5 μg L^-1). Virus abundance varied from 0.37 × 10⁸ to 117 × 10⁸ virus-like-particle (VLP) mL^-1, with the highest values observed in highly salty aquatic systems. Salinity and heterotrophic bacterial abundance were the main variables positively driving viral abundances in these lagoons. We suggest that, with increased salinity, there is a decrease in the protozoan control on bacterial populations and lower bacterial diversity (higher encounter rates with virus specific hosts), both factors positively affecting virus abundance. Virus production varied from 0.68 × 10⁷ to 56.5 × 10⁷ VLP mL^-1 h^-1 and was regulated by bacterial production and total phosphorus, but it was not directly affected by salinity. The uncoupling between virus abundance and virus production supports that the hypothesis that the lack of grazing pressure on viral and bacterial populations is an important mechanism causing virus abundance to escalate with increasing salt concentrations.

Variability of ultraplankton composition and distribution in an oligotrophic coastal ecosystem of the NW Mediterranean Sea derived from a two-year survey at the single cell level

Ultraplankton [heterotrophic prokaryotes and ultraphytoplankton (<10 μm)] were monitored weekly over two years (2009 & 2010) in a coastal area of the NW Mediterranean Sea. Six clusters were differentiated by flow cytometry on the basis of their optical properties, two heterotrophic prokaryote (HP) subgroups labelled LNA and HNA (low and high nucleic acid content respectively), Prochlorococcus, Synechococcus, autotrophic picoeukaryotes and nanoeukaryotes. HP represented an important component of the microbial assemblage over the survey with relatively small abundance variation through seasons. The carbon biomass ratio HP/ultraphytoplankton averaged 0.45, however this ratio exceeded 1 during spring. Ultraphytoplankton biomass made about 50% of the total autotrophic carbon estimates but this contribution increased up to 97% and 67% during the 2009 and 2010 spring periods respectively. Within ultraphytoplankton, nanoeukaryote represent the most important ultraphytoplankton group in terms of autotrophic carbon biomass (up to 70%). Picoeukaryote maximum abundance occurred in winter. Synechococcus was the most abundant population (maximum 1.2 x 10 5 cells cm-3) particularly in spring where it represented up to 54% of ultraphytoplankton carbon biomass. The warmer winter-spring temperatures and the lengthening of the stratification period created a favorable situation for the earlier appearance of Synechococcus and its persistence throughout summer, paralleling Prochlorococcus development. Prochlorococcus was dominant over summer and autumn with concentrations up to 1.0 × 10 5 cells cm-3. While the abundance of Synechococcus throughout survey was of the same order as that reported in western Mediterranean Sea, Prochlorococcus was more abundant and similar to the more typical oligotrophic and warm waters. The abundance variation of the ultraplankton components through the survey was relatable to variations in the hydrological and nutrient conditions.