Pelagic Microbial Communities Research Articles

Drivers of pelagic and benthic microbial communities on Central Arctic seamounts

Seamounts are abundant features on the seafloor that serve as hotspots and barriers for the dispersal of benthic organisms. The primary focus of seamount ecology has typically been on the composition and distribution of faunal communities, with far less attention given to microbial communities. Here, we investigated the microbial communities in the water column (0-3400 m depth) and sediments (619-3883 m depth, 0-16 cm below seafloor) along the ice-covered Arctic ridge system called the Langseth Ridge. We contextualized the microbial community composition with data on the benthic trophic state (i.e., organic matter, chlorophyll-a content, and porewater geochemistry) and substrate type (i.e., sponge mats, sediments, basaltic pebbles). Our results showed slow current velocities throughout the water column, a shift in the pelagic microbial community from a dominance of Bacteroidia in the 0-10 m depth towards Proteobacteria and Nitrososphaeria below the epipelagic zone. In general, the pelagic microbial communities showed a high degree of similarity between the Langseth Ridge seamounts to a northern reference site. The only notable differences were decreases in richness between ~600 m and the bottom waters (~10 m above the seafloor) that suggest a pelagic-benthic coupling mediated by filter feeding of sponges living on the seamount summits. On the seafloor, the sponge spicule mats, and polychaete worms were the principal source of variation in sedimentary biogeochemistry and the benthic microbial community structure. The porewater signature suggested that low organic matter degradation rates are accompanied by a microbial community typical of deep-sea oligotrophic environments, such as Proteobacteria, Acidimicrobiia, Dehalococcoidia, Nitrospira, and archaeal Nitrososphaeria. The combined analysis of biogeochemical parameters and the microbial community suggests that the sponges play a significant role for pelagic-benthic coupling and acted as ecosystem engineers on the seafloor of ice-covered seamounts in the oligotrophic central Arctic Ocean.

Desiccation of ecosystem-critical microbialites in the shrinking Great Salt Lake, Utah (USA)

Great Salt Lake hosts an ecosystem that is critical to migratory birds and international aquaculture, yet it is currently threatened by falling lake elevation and high lakewater salinity resulting from water diversions in the upstream watershed and the enduring megadrought in the western United States. Microbialite reefs underpin the ecosystem, hosting a surface microbial community that is estimated to contribute 30% of the lake’s primary productivity. We monitored exposure, desiccation, and bleaching over time in an area of microbialite reef. During this period, lake elevation fell by 1.8 m, and salinity increased from 11.0% to 19.5% in open-water portions of the outer reef, reaching halite saturation in hydrologically closed regions. When exposed, microbialite bleaching was rapid. Bleached microbialites are not necessarily dead, however, with communities and chlorophyll persisting beneath microbialite surfaces for several months of exposure and desiccation. However, superficial losses in the mat community resulted in enhanced microbialite weathering. In microbialite recovery experiments with bleached microbialite pieces, partial community recovery was rapid at salinities ≤ 17%. 16S and 18S rRNA gene sequencing indicated that recovery was driven by initial seeding from lakewater. At higher salinity levels, eventual accumulation of chlorophyll may reflect accumulation and preservation of lake material in halite crusts vs. true recovery. Our results indicate that increased water input should be prioritized in order to return the lake to an elevation that submerges microbialite reefs and lowers salinity levels. Without quick action to reverse diversions in the watershed, loss of pelagic microbial community members due to sustained high salinity could prevent the recovery of the ecosystem-critical microbialite surface communities in Great Salt Lake.

Microbial Biofilm Colonizing Plastic Substrates in the Ross Sea (Antarctica): First Overview of Community-Level Physiological Profiles

The microbial colonization of plastic substrates made of polyvinylchloride (PVC) and polyethylene (PE) was studied in Tethys and Road Bays (Ross Sea, Antarctica) in order to evaluate the metabolic profiles of the plastisphere community in comparison with those of the surrounding waters. PVC and PE panels, mounted on stainless steel structures, were deployed in the austral summer 2017 at 5 and 20 m and recovered one year later at four different stations (Amorphous Glacier-AG was potentially impacted by the ice-melting process, and its control site was within Tethys Bay-TB; Road Bay-RB, close to the wastewater plant of the Italian research station Mario Zucchelli and its control site Punta Stocchino-PTS). Additional panels were settled in Road Bay at 5 m and recovered after three months to follow time variability in the microbial colonization process. At the same times and depths as plastic substrates, water samples were also collected. Carbon substrates’ utilization rates were determined on scraped microbial biofilm and water samples, with a fluorimetric assay based on 96-well Biolog Ecoplates. Complex carbon sources, carbohydrate and amines were the organic substrates that mostly fuelled the community metabolism in the RB area, while in the TB area, in addition to carbohydrates, phosphate carbon compounds and amino acids were also actively utilized. Within Road Bay, small differences in the physiological profiles were found, with higher metabolic rates in the biofilm community after 3 months’ deployment (late austral summer period) compared to 12 months, suggesting that autumn to spring period conditions negatively affected foulers’ metabolism. Moreover, different metabolic profiles between the plastisphere and the pelagic microbial community were observed; this last utilized a higher number of carbon sources, while plastic substrates were colonized by a more specialized community. Higher carbon substrate utilization rates were recorded at RB and AG stations, receiving organic supply from anthropic activity or ice melting sources, respectively, compared to their control sites. These results highlighted the functional plasticity of the microbial community, with the adaptive ability to utilize a diversified range of organic substrates.

Abundance and microbial diversity from surface to deep water layers over the Rio Grande Rise, South Atlantic

Marine microbes control the flux of matter and energy essential for life in the oceans. Until now, the distribution and diversity of planktonic microorganisms above Fe-Mn crusts have received relatively little attention. Future deep-sea mining is predicted to affect microbial diversity. Here, we studied the ecology of picoplankton among pelagic zones of a Fe-Mn deposit region, at Rio Grande Rise, Southwestern Atlantic Ocean. We investigated microbial community composition using high-throughput sequencing of 16S rRNA genes and their abundance estimated by flow cytometry.The picoplankton populations were more abundant in epi- and mesopelagic waters, corresponding to the Tropical and South Atlantic Central Water masses. Bacterial groups related to heterotrophy, such as Oceanospirillales (Gammapoteobacteria), SAR11 (Alphapoteobacteria), Flavobacteriales (Bacteroida), and Rhodobacterales (Alphapoteobacteria), were the main representatives of the pelagic microbial community. Additionally, we detected abundant assemblages belonging to acetate-oxidizing manganese reducers, i.e., Alteromonas. No differences were observed in microbial community diversity among pelagic zones and water masses. These results provide the first insights into the picoplankton abundance, taxonomy and diversity, and ecological processes in the Rio Grande Rise of the Atlantic Ocean. This may also support draft regulations for deep-sea mining in the region.

Microbial perspective on the giant carbonate ridge Alpha Crucis (Southwestern Atlantic upper slope).

Deep-sea carbonate mounds can harbor a wide variety of heterotrophic and chemosynthetic microbial communities, providing biodiversity hotspots among the deep-sea benthic ecosystems. This study examined the bacterial and archaeal diversity and community structure in the water column and sediments associated with a recently described giant carbonate mound named Alpha Crucis Carbonate Ridge (ACCR), located in the Southwestern Atlantic Ocean. Because of the acoustic evidence of gas chimneys from a previous study, we further evaluated the chemosynthetic primary production through in situ-simulated dark carbon fixation rates. Pelagic microbial communities varied significantly with depth, showing a high abundance of photosynthetic groups in surface waters and taxa related to nitrification in intermediate and deep waters. The benthic communities from the top of the ACCR were very similar along with the sediment depth, while those from the base of the ACCR showed a clear stratification pattern, with members in the deep strata mainly related to anoxic and chemosynthetic ecosystems. Dark carbon fixation rates were of the same order of magnitude as those of deep-sea cold seeps and hydrothermal vents. Our study provides the first description of the ACCR microbiome and adds new information to help formulate and implement future conservation and management strategies for vulnerable marine ecosystems.

Erratum to: On the Possibility of Aerobic Methane Production by Pelagic Microbial Communities of the Laptev Sea

Erratum to: On the Possibility of Aerobic Methane Production by Pelagic Microbial Communities of the Laptev Sea

Aquatic Ecosystems of the Anthropocene: Limnology and Microbial Ecology of Mine Pit Lakes.

Mine pit lakes (‘pit lakes’) are new aquatic ecosystems of the Anthropocene. Potentially hundreds of meters deep, these lakes are prominent in the landscape and in the public consciousness. However, the ecology of pit lakes is underrepresented in the literature. The broad goal of this research was to determine the environmental drivers of pelagic microbe assemblages in Australian coal pit lakes. The overall experimental design was four lakes sampled three times, top and bottom, in 2019. Instrument chains were installed in lakes and measurements of in situ water quality and water samples for metals, metalloids, nutrients and microbe assemblage were collected. Lakes were monomictic and the timing of mixing was influenced by high rainfall events. Water quality and microbial assemblages varied significantly across space and time, and most taxa were rare. Lakes were moderately saline and circumneutral; Archeans were not prevalent. Richness also varied by catchment. Microbial assemblages correlated to environmental variables, and no one variable was consistently significant, spatially or temporally. Study lakes were dominated by ‘core’ taxa exhibiting temporal turnover likely driven by geography, water quality and interspecific competition, and the presence of water chemistry associated with an artificial aquifer likely influenced microbial community composition. Pit lakes are deceptively complex aquatic ecosystems that host equally complex pelagic microbial communities. This research established links between microbial assemblages and environmental variables in pit lakes and determined core communities; the first steps towards developing a monitoring program using microbes.

Climate Projections for the Southern Ocean Reveal Impacts in the Marine Microbial Communities Following Increases in Sea Surface Temperature

Anthropogenic global warming can have strong impacts on marine ecosystems, especially on climate-sensitive regions such as the Southern Ocean (SO). As key drivers of biogeochemical cycles, pelagic microbial communities are likely to respond to increases in sea surface temperature (SST). Thus, it is critical to understand how SST may change in future scenarios and how these changes will affect the composition and structure of microbial communities. By using a suite of Earth System Models participating in the Coupled Model Intercomparison Project Phase 6 (CMIP6), machine learning, and 16S rRNA sequencing data, we investigated the long-term changes as projected by CMIP6 simulations in SST throughout the twenty first century and the microbial diversity responses in the SO. Four Shared Socioeconomic Pathways (SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5) were considered to assess the SO surface sensitivity to a warming climate. The SST changes across SSPs were ≈0.3, ≈0.7, ≈1.25, and ≈1.6oC between 2015 and 2100, respectively, and the high emissions scenarios projected a much sooner emergence of the human-induced temperature change throughout the SO. The impacts on Antarctic marine diversity of bacteria and archaea are expected to be significant and persistent by the late twenty first century, especially within the higher end of the range of future forcing pathways.

Selective Uptake of Pelagic Microbial Community Members by Caribbean Reef Corals.

Coral reefs are possible sinks for microbes; however, the removal mechanisms at play are not well understood. Here, we characterize pelagic microbial groups at the CARMABI reef (Curaçao) and examine microbial consumption by three coral species: Madracis mirabilis, Porites astreoides, and Stephanocoenia intersepta Flow cytometry analyses of water samples collected from a depth of 10 m identified 6 microbial groups: Prochlorococcus, three groups of Synechococcus, photosynthetic eukaryotes, and heterotrophic bacteria. Minimum growth rates (μ) for Prochlorococcus, all Synechococcus groups, and photosynthetic eukaryotes were 0.55, 0.29, and 0.45 μ day-1, respectively, and suggest relatively high rates of productivity despite low nutrient conditions on the reef. During a series of 5-h incubations with reef corals performed just after sunset or prior to sunrise, reductions in the abundance of photosynthetic picoeukaryotes, Prochlorococcus and Synechococcus cells, were observed. Of the three Synechococcus groups, one decreased significantly during incubations with each coral and the other two only with M. mirabilis. Removal of carbon from the water column is based on coral consumption rates of phytoplankton and averaged between 138 ng h-1 and 387 ng h-1, depending on the coral species. A lack of coral-dependent reduction in heterotrophic bacteria, differences in Synechococcus reductions, and diurnal variation in reductions of Synechococcus and Prochlorococcus, coinciding with peak cell division, point to selective feeding by corals. Our study indicates that bentho-pelagic coupling via selective grazing of microbial groups influences carbon flow and supports heterogeneity of microbial communities overlying coral reefs.IMPORTANCE We identify interactions between coral grazing behavior and the growth rates and cell abundances of pelagic microbial groups found surrounding a Caribbean reef. During incubation experiments with three reef corals, reductions in microbial cell abundance differed according to coral species and suggest specific coral or microbial mechanisms are at play. Peaks in removal rates of Prochlorococcus and Synechococcus cyanobacteria appear highest during postsunset incubations and coincide with microbial cell division. Grazing rates and effort vary across coral species and picoplankton groups, possibly influencing overall microbial composition and abundance over coral reefs. For reef corals, use of such a numerically abundant source of nutrition may be advantageous, especially under environmentally stressful conditions when symbioses with dinoflagellate algae break down.

On the Possibility of Aerobic Methane Production by Pelagic Microbial Communities of the Laptev Sea

—The taxonomic diversity and metabolic activity of microbial communities in the Laptev Sea water column above and outside the methane seep field were studied. The concentrations of dissolved methane in the water column at both stations were comparable until the depth of the pycnocline (25 m). At this depth, local methane maxima were recorded, with the highest concentration (116 nM CH4) found at the station outside the methane seep field. Results of the 16S rRNA gene sequencing and measurements of the rates of hydrogenotrophic methanogenesis indicated the absence of methanogenesis caused by the methanogenic archaea in the pycnocline and in other horizons of the water column. The 16S rRNA-based analysis of microbial phylogenetic diversity, as well as radiotracer analysis of the rates of primary production (PP), dark CO2 assimilation (DCA), and methane oxidation (MO), indicated the functioning of a diverse community of pelagic microorganisms capable of transforming a wide range of organic compounds under oligotrophic conditions of the Arctic basin. Hydrochemical prerequisites and possible microbial agents of aerobic methane production via demethylation of methylphosphonate and decomposition of dimethylsulfoniopropionate using dissolved organic matter synthesized in the PP, DCA, and MO processes are discussed.

Terrestrial Inputs Shape Coastal Bacterial and Archaeal Communities in a High Arctic Fjord (Isfjorden, Svalbard).

The Arctic is experiencing dramatic changes including increases in precipitation, glacial melt, and permafrost thaw, resulting in increasing freshwater runoff to coastal waters. During the melt season, terrestrial runoff delivers carbon- and nutrient-rich freshwater to Arctic coastal waters, with unknown consequences for the microbial communities that play a key role in determining the cycling and fate of terrestrial matter at the land-ocean interface. To determine the impacts of runoff on coastal microbial (bacteria and archaea) communities, we investigated changes in pelagic microbial community structure between the early (June) and late (August) melt season in 2018 in the Isfjorden system (Svalbard). Amplicon sequences of the 16S rRNA gene were generated from water column, river and sediment samples collected in Isfjorden along fjord transects from shallow river estuaries and glacier fronts to the outer fjord. Community shifts were investigated in relation to environmental gradients, and compared to river and marine sediment microbial communities. We identified strong temporal and spatial reorganizations in the structure and composition of microbial communities during the summer months in relation to environmental conditions. Microbial diversity patterns highlighted a reorganization from rich communities in June toward more even and less rich communities in August. In June, waters enriched in dissolved organic carbon (DOC) provided a niche for copiotrophic taxa including Sulfitobacter and Octadecabacter. In August, lower DOC concentrations and Atlantic water inflow coincided with a shift toward more cosmopolitan taxa usually associated with summer stratified periods (e.g., SAR11 Clade Ia), and prevalent oligotrophic marine clades (OM60, SAR92). Higher riverine inputs of dissolved inorganic nutrients and suspended particulate matter also contributed to spatial reorganizations of communities in August. Sentinel taxa of this late summer fjord environment included taxa from the class Verrucomicrobiae (Roseibacillus, Luteolibacter), potentially indicative of a higher fraction of particle-attached bacteria. This study highlights the ecological relevance of terrestrial runoff for Arctic coastal microbial communities and how its impacts on biogeochemical conditions may make these communities susceptible to climate change.

Characterization of marine microbial communities around an Arctic seabed hydrocarbon seep at Scott Inlet, Baffin Bay

Seabed hydrocarbon seeps present natural laboratories for investigating responses of marine ecosystems to petroleum input. A hydrocarbon seep near Scott Inlet, Baffin Bay, was visited for in situ observations and sampling in the summer of 2018. Video evidence of an active hydrocarbon seep was confirmed by methane and hydrocarbon analysis of the overlying water column, which is 260 m at this site. Elevated methane concentrations in bottom water above and down current from the seep decreased to background seawater levels in the mid-water column >150 m above the seafloor. Seafloor microbial mats morphologically resembling sulfide-oxidizing bacteria surrounded areas of bubble ebullition. Calcareous tube worms, brittle stars, shrimp, sponges, sea stars, sea anemones, sea urchins, small fish and soft corals were observed near the seep, with soft corals showing evidence for hydrocarbon incorporation. Sediment microbial communities included putative methane-oxidizing Methyloprofundus, sulfate-reducing Desulfobulbaceae and sulfide-oxidizing Sulfurovum. A metabolic gene diagnostic for aerobic methanotrophs (pmoA) was detected in the sediment and bottom water above the seep epicentre and up to 5 km away. Both 16S rRNA gene and pmoA amplicon sequencing revealed that pelagic microbial communities oriented along the geologic basement rise associated with methane seepage (running SW to NE) differed from communities in off-axis water up to 5 km away. Relative abundances of aerobic methanotrophs and putative hydrocarbon-degrading bacteria were elevated in the bottom water down current from the seep. Detection of bacterial clades typically associated with hydrocarbon and methane oxidation highlights the importance of Arctic marine microbial communities in mitigating hydrocarbon emissions from natural geologic sources.

A novel real-world ecotoxicological dataset of pelagic microbial community responses to wastewater

Real-world observational datasets that record and quantify pressure-stressor-response linkages between effluent discharges and natural aquatic systems are rare. With global wastewater volumes increasing at unprecedented rates, it is urgent that the present dataset is available to provide the necessary information about microbial community structure and functioning. Field studies were performed at two time-points in the Austral summer. Single-species and microbial community whole effluent toxicity (WET) testing was performed at a complete range of effluent concentrations and two salinities, with accompanying environmental data to provide new insights into nutrient and organic matter cycling, and to identify ecotoxicological tipping points. The two salinity regimes were chosen to investigate future scenarios based on a predicted salinity increase at the study site, typical of coastal regions with rising sea levels globally. Flow cytometry, amplicon sequencing of 16S and 18S rRNA genes and micro-fluidic quantitative polymerase-chain reactions (MFQPCR) were used to determine chlorophyll-a and total bacterial cell numbers and size, as well as taxonomic and functional diversity of pelagic microbial communities. This strong pilot dataset could be replicated in other regions globally and would be of high value to scientists and engineers to support the next advances in microbial ecotoxicology, environmental biomonitoring and estuarine water quality modelling.

Bubble-mediated transport of benthic microorganisms into the water column: Identification of methanotrophs and implication of seepage intensity on transport efficiency

Benthic microorganisms transported into the water column potentially influence biogeochemical cycles and the pelagic food web structure. In the present study six gas-releasing vent sites in the Coal Oil Point seep field (California) were investigated, and the dislocation of microorganisms from the sediment into the water column via gas bubbles released from the seabed was documented. It was found that the methanotrophs transport efficiency was dependent on the volumetric gas flow, with the highest transport rate of 22.7 × 103 cells mLgas−1 at a volumetric gas flow of 0.07 mLgas s−1, and the lowest rate of 0.2 × 103 cells mLgas−1 at a gas flow of 2.2 mLgas s−1. A simple budget approach showed that this bubble-mediated transport has the potential to maintain a relevant part of the water-column methanotrophs in the seep field. The bubble-mediated link between the benthic and pelagic environment was further supported by genetic analyses, indicating a transportation of methanotrophs of the family Methylomonaceae and oil degrading bacteria of the genus Cycloclasticus from the sediment into the water column. These findings demonstrate that the bubble-mediated transport of microorganisms influences the pelagic microbial abundance and community composition at gas-releasing seep sites.

Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry.

SummaryThe Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI‐B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by a Chloroflexi oligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to an Actinobacteria oligotype (acI‐C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations.

Bacterial community rather than metals shaping metal resistance genes in water, sediment and biofilm in lakes from arid northwestern China

Lakes in arid northwestern China are valuable freshwater resources that drive socioeconomic development. Environmental pollution can significantly influence the composition of microbial communities and the distribution of functional genes in lakes. This study investigated heavy metal pollution to identify possible correlations with metal resistance genes (MRGs) and bacterial community composition in water, sediment and biofilm samples from Bosten Lake and Ebi Lake in northwestern China. High levels of zinc were detected in all samples. However, the metals detected in the sediment samples of both lakes were determined to be at low risk levels according to an ecological index. The mercury resistance gene subtype merP had the greatest average abundance (4.61 × 10−3 copies per 16S rRNA) among all the samples, followed by merA and merC. The high abundance of merA in the pelagic zone rather than in benthic sediment suggests that the pelagic microbial community was important in mercury reduction. Proteobacteria were the main phylum found in the microbial communities in all samples. However, microbial communities in most of the water, sediment and biofilm samples had different compositions, indicating that the habitat niche plays an important role in shaping the bacterial communities in lakes. The microbial community, rather than the heavy metals, was the main driver of MRG distribution. The abundances of some bacterial genera involved in the decomposition of organic matter and the terrestrial nitrogen cycle were negatively correlated with heavy metals. This result suggests that metal pollution can adversely affect the biogeochemical processes that occur in lakes.

Seasonality of the antibiotic resistance gene blaCTX-M in temperate Lake Maggiore

The beta lactamase gene blaCTX-M, responsible of the resistance to cephalosporins, has been detected in microbes from hospitals to open waters. We studied the seasonality and stability of blaCTX-M in Lake Maggiore over 3 years and the role of potential inputs of allochthonous bacteria and/or antibiotic pollution in promoting its occurrence. blaCTX-M was mainly present from January to July in the pelagic microbial community and the gene occurrence was significantly related to low water temperature. To evaluate its temporal stability in the bacterial community over a short period, we measured blaCTX-M daily over the course of 6 days. The gene was below the limit of quantification except for one sampling when its abundance peaked, suggesting a point contamination. The bacterial community of the lake in which blaCTX-M was detected suggests that at least two distinct bacterial populations contained the gene. The occurrence of known blaCTX-M containing genera and the occurrence of the gene, however, did not overlap. Furthermore, the experimental addition of cefotaxime to lake water incubations did not promote abundance of the gene. These data imply that blaCTX-M was present in the environmental microbial community. Increases of gene abundances were likely caused by environmental parameters other than antibiotic contamination.

Lack of ciliate community integrity in transitional waters: A case study from the Baltic Sea

The Baltic Sea, one of the world's largest brackish water environments, is particularly suitable for studies aiming to understand biodiversity in saltwater–freshwater mixing zones, i.e., transitional waters at different spatial and temporal scales. To evaluate diversity fluctuations in the pelagic microbial communities experiencing frequent brackish water intrusions, we analyzed seasonal dynamics of ciliates inhabiting transitional waters of the Curonian Lagoon. During the intrusion periods, the community presented a mixture of fresh- and brackish taxa, with no specific autochthonous component unique to the transitional waters. In the plume area, outside of the lagoon, we found that (i) high biodiversity was due to mixing of two distinct assemblages, and (ii) freshwater taxa are rather resistant to salinity change, their abundance decreases almost linearly with the increasing salinity, following conservative mixing model. Small unidentified Lohmanniella occurring exclusively in the plume zone during our survey possibly presents an autochthonous component based on locally available resource. Also mixed assemblage of the plume is characterised by absence of large predatory ciliate species.

Pigments in surface sediments of South American shallow lakes as an integrative proxy for primary producers and their drivers

Abstract Pigments in lake surface sediments integrate both benthic and pelagic primary producer composition at the whole‐lake ecosystem level. We gathered a comprehensive set of water chemistry, morphometric, physical and biological lake variables, catchment and climate characteristics, and geographical descriptors. We used multiple regressions to relate whole‐lake algal pigment concentration to environmental conditions and multivariate statistical analyses to assess the factors most associated with photoautotrophic algal and bacterial community composition. The relative influence of environmental factors and spatial distribution was assessed by variance partitioning analysis among three groups of variables: (1) in‐lake factors, (2) external factors, and (3) geographic descriptors. Pigment concentration and community composition were most sensitive to in‐lake factors. Pigment‐inferred abundance of algae, including cyanobacteria, tended to be highest in shallower systems with high nutrient concentrations, independent of the latitudinal temperature or irradiance gradients. Pigment‐inferred community composition was best explained by nutrients and biotic composition (zooplankton and fish communities). Only in maritime temperate lakes did a link with regional location occur due to their low dissolved inorganic nitrogen to soluble reactive phosphorus ratios (1.5 atomic ratio), suggesting nitrogen limitation of phytoplankton growth; accordingly, the sediment pigments revealed cyanobacteria to be the dominant group, although this may also be a consequence of the overall high nutrient levels in these lakes. Despite the large climate gradient covered, in‐lake rather than external factors were associated with the patterns observed in pigment concentration (from benthic and pelagic microorganisms) and inferred composition and abundance in these shallow lakes. Our results suggest that pigment assemblages in sediments, which integrate both benthic and pelagic microbial photoautotrophic community and processes, are valuable indicators of changes in shallow (0.75–12 m depth) lake ecosystems.

Recent changes in the spring microplankton of Lake Baikal, Russia

Lake Baikal is facing several environmental stressors, including climate change and nearshore eutrophication. To assess recent ecological changes in Lake Baikal and provide a baseline for future comparisons, we sampled spring plankton communities from the pelagic zone of the lake in 2016 and compared these data with unpublished and published historical information going back to 1990. In 2016, one pelagic long-term monitoring station was sampled in early spring (March) during ice cover and 21 long-term monitoring stations located throughout the lake were sampled in late spring (May-June). We measured water chemistry parameters at most stations and the abundance, taxonomic composition and biomass of bacteria, ciliates and phytoplankton at several locations in different areas of the lake. Biotic parameters from 2016 were compared with historical data, showing significant changes in the spring pelagic microbial community since the 1990s. We show increased quantities of small species, mixotrophic ciliates, and the appearance (or increasing number) of small coloured and colourless flagellates. We also show substantially decreased densities of formerly dominant heavily silicified diatoms such as Aulacoseira spp. Since 2007, Synedra acus subsp. radians, a smaller and weakly silicified diatom, has dominated the spring plankton of the lake. These results suggest that Lake Baikal’s pelagic plankton community may be changing, with climate likely playing a dominant role in these changes.