Planktonic Microbial Assemblages Research Articles

Response of planktonic microbial assemblages to disturbance in an urban sub-tropical estuary.

Microbes are sensitive indicators of estuarine processes because they respond rapidly to dynamic disturbance events. As most of the world's population lives in urban areas and climate change-related disturbance events are becoming more frequent, estuaries bounded by cities are experiencing increasing stressors, at the same time that their ecosystem services are required more than ever. Here, using a multidisciplinary approach, we determined the response of planktonic microbial assemblages in response to seasonality and a rainfall disturbance in an urban estuary bounded by Australia's largest city, Sydney. We used molecular barcoding (16S, 18S V4 rRNA) and microscopy-based identification to compare microbial assemblages at locations with differing characteristics and urbanisation histories. Across 142 samples, we identified 8,496 unique free-living bacterial zOTUs, 8,175 unique particle associated bacterial zOTUs, and 1,920 unique microbial eukaryotic zOTUs. Using microscopy, we identified only the top <10% abundant, larger eukaryotic taxa (>10µm), however quantification was possible. The site with the greater history of anthropogenic impact showed a more even community of associated bacteria and eukaryotes, and a significant increase in dissolved inorganic nitrogen following rainfall, when compared to the more buffered site. This coincided with a reduced proportional abundance of Actinomarina and Synechococcus spp., a change in SAR 11 clades, and an increase in the eukaryotic microbial groups Dinophyceae, Mediophyceae and Bathyoccocaceae, including a temporary dominance of the harmful algal bloom dinoflagellate Prorocentrum cordatum (syn. P. minimum). Finally, a validated hydrodynamic model of the estuary supported these results, showing that the more highly urbanised and upstream location consistently experienced a higher magnitude of salinity reduction in response to rainfall events during the study period. The best abiotic variables to explain community dissimilarities between locations were TDP, PN, modelled temperature and salinity (r=0.73) for the free living bacteria, TP for the associated bacteria (r=0.43), and modelled temperature (r=0.28) for the microbial eukaryotic communities. Overall, these results show that a minor disturbance such as a brief rainfall event can significantly shift the microbial assemblage of an anthropogenically impacted area within an urban estuary to a greater degree than a seasonal change, but may result in a lesser response to the same disturbance at a buffered, more oceanic influenced location. Fine scale research into the factors driving the response of microbial communities in urban estuaries to climate related disturbances will be necessary to understand and implement changes to maintain future estuarine ecosystem services.

Local-Scale Damming Impact on the Planktonic Bacterial and Eukaryotic Assemblages in the upper Yangtze River.

Dam construction and impoundment cause discontinuities in the natural biophysical gradients in rivers. These discontinuities may alter distinctive habitats and different microbial community assembly mechanisms upstream and downstream of dams, which reflect the potential impacts of damming on riverine aquatic ecosystems. In this study, we investigated the planktonic microbial assemblages of three large dams in the upper Yangtze River by using high-throughput sequencing. The results revealed that the alpha diversity indexes increased downstream of the dams. In addition, more eukaryotic ASVs solely occurred downstream of the dams, which indicated that a large proportion of eukaryotes appeared downstream of the dams. The nonmetric multidimensional scaling analysis indicated that there was no obvious geographic clustering of the planktonic microbial assemblages among the different locations or among the different dams. However, the dam barriers changed dam-related variables (maximum dam height and water level) and local environmental variables (water temperature, DOC, etc.) that could possibly affect the assembly of the planktonic microbial communities that are closest to the dams. A co-occurrence network analysis demonstrated that the keystone taxa of the planktonic bacteria and eukaryotes decreased downstream of the dams. In particular, the keystone taxa of the eukaryotes disappeared downstream of the dams. The robustness analysis indicated that the natural connectivity of the microbial networks decreased more rapidly upstream of the dams, and the downstream eukaryotic network was more stable. In conclusion, damming has a greater impact on planktonic eukaryotes than on bacteria in near-dam areas, and planktonic microbial assemblages were more susceptible to the environmental changes. Our study provides a better understanding of the ecological effects of river damming.

Depth-Differentiation and Seasonality of Planktonic Microbial Assemblages in the Monterey Bay Upwelling System.

Coastal upwelling regions are hotspots of biological productivity, supporting diverse communities of microbial life and metabolisms. Monterey Bay (MB), a coastal ocean embayment in central California, experiences seasonal upwelling of cold, nutrient-rich waters that sustain episodes of high phytoplankton production in surface waters. While productivity in surface waters is intimately linked to metabolisms of diverse communities of Archaea and Bacteria, a comprehensive understanding of the microbial community in MB is missing thus far, particularly in relation to the distinct hydrographic seasons characteristic of the MB system. Here we present the results of a 2-year microbial time-series survey in MB, investigating community composition and structure across spatiotemporal gradients. In deciphering these patterns, we used unique sequence variants (SVs) of the 16S rRNA gene (V4–V5 region), complemented with metagenomes and metatranscriptomes representing multiple depth profiles. We found clear depth-differentiation and recurring seasonal abundance patterns within planktonic communities, particularly when analyzed at finer taxonomic levels. Compositional changes were more pronounced in the upper 0–40 m of the water column, whereas deeper depths were characterized by temporally stable populations. In accordance with the dynamic nutrient profiles, the system appears to change from a Bacteroidetes- and Rhodobacterales-dominated upwelling period to an oceanic season dominated by oligotrophic groups such as SAR11 and picocyanobacteria. The cascade of environmental changes brought about by upwelling and relaxation events thus impacts microbial community structure in the bay, with important implications for the temporal variability of nutrient and energy fluxes within the MB ecosystem. Our observations emphasize the need for continued monitoring of planktonic microbial communities in order to predict and manage the behavior of this sensitive marine sanctuary ecosystem, over projected intensification of upwelling in the region.

Inorganic mercury (Hg2+) accumulation in autotrophic and mixotrophic planktonic protists: Implications for Hg trophodynamics in ultraoligotrophic Andean Patagonian lakes

Microbial assemblages are typical of deep ultraoligotrophic Andean Patagonian lakes and comprise picoplankton and protists (phytoflagellates and mixotrophic ciliates), having a central role in the C cycle, primary production and in the incorporation of dissolved inorganic mercury (Hg2+) into lake food webs. In this study we evaluated the mechanisms of Hg2+ incorporation in hetero- and autotrophic bacteria, in the autotrophic dinoflagellate (Gymnodinium paradoxum) and in two mixotrophic ciliates (Stentor araucanus and Ophrydium naumanni) dominating the planktonic microbial assemblage. The radioisotope 197Hg was used to trace the Hg2+ incorporation in microbiota. Hg uptake was analyzed as a function of cell abundance (BCF: bioconcentration factor), cell surface (SCF: surface concentration factor) and cell volume (VCF: volume concentration factor). Overall, the results obtained showed that these organisms incorporate substantial amounts of dissolved Hg2+ passively (adsorption) and actively (bacteria consumption or attachment), displaying different Hg internalization and therefore, varying potential for Hg transfer. Surface area and quality, and surface:volume ratio (S:V) control the passive uptake in all the organisms. Active incorporation depends on bacteria consumption in the mixotrophic ciliates, or on bacteria association to surface in the autotrophic dinoflagellate. Hg bioaccumulated by pelagic protists can be transferred to higher trophic levels through plankton and fish feeding, regenerated to the dissolved phase by excretion, and/or transferred to the sediments by particle sinking. In ultraoligotrophic Andean Patagonian lakes, picoplankton and planktonic protists are key components of lake food webs, linking the pelagic and benthic Hg pathways, and thereby playing a central role in Hg trophodynamics.

Coaggregation in a microbial predator–prey system affects competition and trophic transfer efficiency

Emerging interactions are key determinants of system productivity and efficiency in plant and animal communities, whereas their importance for planktonic microbial assemblages is unknown. We studied the relationship between two aquatic bacterial strains and a protistan predator with respect to cooperation and system efficiency. While competitive exclusion of one bacterial strain was observed in grazer‐free cocultures, the presence of the predator induced the formation of large coaggregates and allowed a coexistence of both strains. The aggregates moreover provided a substrate for attachment of the predators. The interactions in the more complex community, i.e., microbial flocs composed by both bacterial strains and predators, led to a significantly increased transfer efficiency of dissolved organic matter to the higher trophic level than in systems with two species only. Similar emerging interactions might also play a role in complex microbial assemblages in natural aquatic systems, i.e., on suspended organic aggregates.

Environmental dynamics as a structuring factor for microbial carbon utilization in a subtropical coastal lagoon.

Laguna de Rocha belongs to a series of shallow coastal lagoons located along South America. It is periodically connected to the sea through a sand bar, exhibiting a hydrological cycle where physicochemical and biological gradients are rapidly established and destroyed. Its most frequent state is the separation of a Northern zone with low salinity, high turbidity and nutrient load, and extensive macrophyte growth, and a Southern zone with higher salinity and light penetration, and low nutrient content and macrophyte biomass. This zonation is reflected in microbial assemblages with contrasting abundance, activity, and community composition. The physicochemical conditions exerted a strong influence on community composition, and transplanted assemblages rapidly transformed to resembling the community of the recipient environment. Moreover, the major bacterial groups responded differently to their passage between the zones, being either stimulated or inhibited by the environmental changes, and exhibiting contrasting sensitivities to gradients. Addition of allochthonous carbon sources induced pronounced shifts in the bacterial communities, which in turn affected the microbial trophic web by stimulating heterotrophic flagellates and virus production. By contrast, addition of organic and inorganic nutrient sources (P or N) did not have significant effects. Altogether, our results suggest that (i) the planktonic microbial assemblage of this lagoon is predominantly carbon-limited, (ii) different bacterial groups cope differently with this constraint, and (iii) the hydrological cycle of the lagoon plays a key role for the alleviation or aggravation of bacterial carbon limitation. Based on these findings we propose a model of how hydrology affects the composition of bacterioplankton and of carbon processing in Laguna de Rocha. This might serve as a starting hypothesis for further studies about the microbial ecology of this lagoon, and of comparable transitional systems.

Water Quality and Planktonic Microbial Assemblages of Isolated Wetlands in an Agricultural Landscape

Wetlands provide ecosystem services including flood protection, water quality enhancement, food chain support, carbon sequestration, and support regional biodiversity. Wetlands occur in human-altered landscapes, and the ongoing ability of these wetlands to provide ecosystem services is lacking. Additionally, the apparent lack of connection of some wetlands, termed geographically isolated, to permanent waters has resulted in little regulatory recognition. We examined the influence of intensive agriculture on water quality and planktonic microbial assemblages of intermittently inundated wetlands. We sampled 10 reference and 10 agriculturally altered wetlands in the Gulf Coastal Plain of Georgia. Water quality measures included pH, alkalinity, dissolved organic carbon, nutrients (nitrate, ammonium, and phosphate), and filterable solids (dry mass and ash-free dry mass). We measured abundance and relative size distribution of the planktonic microbial assemblage (<45 μm) using flow cytometry. Water quality in agricultural wetlands was characterized by elevated nutrients, pH, and suspended solids. Autotrophic microbial cells were largely absent from both wetland types. Heterotrophic microbial abundance was influenced by nutrients and suspended matter concentration. Agriculture caused changes in microbial assemblages forming the base of wetland food webs. Yet, these wetlands potentially support important ecological services in a highly altered landscape.

Colonization of overlaying water by bacteria from dry river sediments

We studied the diversity, community composition and activity of the primary microbial colonizers of the water above freshly re-wetted sediments from a temporary river. Dried sediments, collected from Mulargia River (Sardinia, Italy), were covered with sterile freshwater in triplicate microcosms, and changes of the planktonic microbial assemblage were monitored over a 48 h period. During the first 9 h bacterial abundance was low (1.5 x 10(4) cells ml(-1)); it increased to 3.4 x 10(6) cells ml(-1) after 28 h and did not change thereafter. Approximately 20% of bacteria exhibited DNA de novo synthesis already after 9 h of incubation. Changes of the ratios of (3)H-leucine to (3)H-thymidine incorporation rates indicated a shift of growth patterns during the experiment. Extracellular enzyme activity showed a maximum at 48 h with aminopeptidase activity (430.8 +/- 22.6 nmol MCA l(-1) h(-1)) significantly higher than alkaline phosphatase (98.6 +/- 4.3 nmol MUF l(-1) h(-1)). The primary microbial colonizers of the overlaying water - as determined by 16S rRNA gene sequence analysis - were related to at least six different phylogenetic lineages of Bacilli and to Alphaproteobacteria (Brevundimonas spp. and Caulobacter spp.). Large bacterial cells affiliated to one clade of Bacillus sp. were rare in the dried sediments, but constituted the majority of the planktonic microbial assemblage and of cells with detectable DNA-synthesis until 28 h after re-wetting. Their community contribution decreased in parallel with a rise of flagellated and ciliated protists. Estimates based on cell production rates suggested that the rapidly enriched Bacillus sp. suffered disproportionally high loss rates from selective predation, thus favouring the establishment of a more heterogenic assemblage of microbes (consisting of Proteobacteria, Actinobacteria and Cytophaga-Flavobacteria). Our results suggest that the primary microbial colonizers of the water above dried sediments are passively released into the plankton and that their high growth potential is counteracted by the activity of bacterivorous protists.

Planktonic microbial assemblages and the potential effects of metazooplankton predation on the food web of lakes from the maritime Antarctica and sub-Antarctic islands

Antarctica is the continent with the harshest climate on the Earth. Antarctic lakes, however, usually presents liquid water, at least during part of the year or below the ice cover, especially those from the sub-Antarctic islands and the maritime Antarctic region where climatic conditions are less extreme. Planktonic communities in these lakes are mostly dominated by microorganisms, including bacteria and phototrophic and heterotrophic protists, and by metazooplankton, usually represented by rotifers and calanoid copepods, the latter mainly from the genus Boeckella. Here I report and discuss on studies performed during the last decade that show that there is a potential for top–down control of the structure of the planktonic microbial food web in sub-Antarctic and maritime Antarctic lakes. In some of the studied lakes, the effect of copepod grazing on protozoa, either ciliates or flagellates, depending on size of both the predator and the prey, could promote cascade effects that would be transmitted to the bacterioplankton assemblage.

Copepod grazing impact on the trophic structure of the microbial assemblage of the San Pedro Channel, California

In August 2002 and March 2003 the trophic structure of the microbial assemblage from the San Pedro Channel, California was studied following the experimental alteration of the number of copepods. Changes in the abundance/biomass of microorganisms <80 μm during 3-day incubations were monitored in (i) the absence of metazoa >80 μm, (ii) the presence of natural abundances of metazoa and (iii) the presence of an elevated number of copepods. Prokaryotes and small-sized eukaryotes (<4 μm) dominated plankton biomass during both experimental months. Diatoms numerically dominated the 10–80 μm plankton in August 2002, but ciliate and heterotrophic dinoflagellate biomass generally exceeded diatom biomass on both dates. Ingestion of protozooplankton (predominantly ciliates) contributed substantially to copepod daily carbon rations. The adult copepod assemblage removed 4.6 and 36% per day of the microzooplankton standing stocks (10–80 μm size fraction) in August and March, respectively. Elevated copepod grazing pressure on protozooplankton resulted in increased biomass of nanoplankton (<5 μm) presumably via a trophic cascade. Accordingly, the copepod–protozoan trophic link appears to be a key factor structuring the planktonic microbial assemblage in the San Pedro Channel.

Biodiversity in Southeastern, Seasonally Ponded, Isolated Wetlands: Management and Policy Perspectives for Research and Conservation

BRIDGES is a recurring feature of J-NABS intended to provide a forum for the interchange of ideas and information between basic and applied researchers in benthic science. Articles in this series will focus on topical research areas and linkages between basic and applied aspects of research, monitoring policy, and education. Readers with ideas for topics should contact Associate Editors, Nick Aumen and Marty Gurtz. Isolated wetlands have received little attention as a specific ecosystem type, yet many development and regulatory programs affect them. This lack of recognition may stem from their small size, their variable hydrology, and lack of recognition of their regional significance in the southeast US. In recognition of this problem, and in response to a US National Research Council recommendation for more research in support of wetland protection, a group of individuals convened a workshop to discuss information needs and to develop strategies to protect southeastern isolated wetlands and their biodiversity. Because the organizers perceived a lack of linkage between researchers and managers, workshop participants included scientists, natural resource managers of public and private lands, and conservationists.

Contribution of the different planktonic microbial assemblages to ETS activity in the Ligurian frontal area: north-west Mediterranean Sea

Spatial and size distribution of micro-organisms and their ETS activity has been investigated in Ligurian Sea surface waters along the Nice-Calvi transect across frontal areas from 18 to 37 km offshore (TOMOFRONT 1 and 2 cruises, April 1988 and April-May 1989 respectively). Aplastidic and plastidic nanoflagellates and aplastidic picoflagellates were present in numbers close to 0.25 × 104 cells ml−1, whereas plastidic picoflagellates accounted for about half this number. Correlations have been evidenced between plastidic and aplastidic micro-organisms within the same size group, suggesting that they belong to a well-defined ecosystem. The highest correlation between total ETS activity and abundance of the considered size groups was observed for nanoflagellates (r = 0.94, n = 22, and r = 0.90, n = 22 for aplastidic and plastidic cells respectively). The importance of the role of nanoflagellates in surface waters, with respect to the overall ETS activity, was supported by results from size fractionation which assigned to the 3–10 μm size range a 73.3% contribution to overall ETS activity. Results emphasize analysing global ETS activity of natural samples in order to derive relationships between the different populations present in the sampled water. It is suggested that coupling flow cytometry to the ETS approach should be very helpful in that respect.

Microbial uptake of radiolabeled substrates: estimates of growth rates from time course measurements.

The uptake of [3H]glucose and a mixture of 3H-labeled amino acids was measured, in time course fashion, in planktonic microbial assemblages of the eastern tropical Pacific Ocean. The average generation times of those portions of the assemblages able to utilize these substrates were estimated from a simple exponential growth model. Other workers have independently used this model in its integrated or differential form. A mathematical verification and an experimental demonstration of the equivalence of the two approaches are presented. A study was made of the size distribution of heterotrophic activity, using time course measurements. It was found that the size distribution and the effect of sample filtration before radiolabeling were dependent on time of incubation. In principle, it was possible to ascribe these time dependences to differences in the specific growth rate and initial standing stock of the microbial assemblages.