Microbial abundance patterns along a transparency gradient suggest a weak coupling between heterotrophic bacteria and flagellates in eutrophic shallow Pampean lakes

Fermani, Paulina; Torremorell, Ana; Lagomarsino, Leonardo; Escaray, Roberto Ulises; Unrein, Fernando; Pérez, Gonzalo L.

doi:10.1007/s10750-014-2019-x

Cited by 20 publications

(19 citation statements)

References 82 publications

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“…Regarding the spatial presence of the different zOTUs, each Pampean shallow lake was represented by a particular assemblage associated with local environmental factors. These results lend support to previous evidence about the importance of underwater light conditions and the availability of nutrients in governing freshwater picocyanobacterial distribution (35,(64)(65)(66)(67)(68).…”

Section: Discussionsupporting

confidence: 89%

“…(ii) Eight freshwater samples were taken from four hypertrophic shallow lakes (Table S11) of the Salado River floodplain basin, located in the Pampa plain in Argentina (35°41=S, 59°35=W) (22,68). The samples were selected in order to cover spatial and temporal variation.…”

Section: Methodsmentioning

confidence: 99%

“…In addition, five samples from Chascomús lake were collected between October 2012 and May 2014 (Table S11). Site features and sampling details are provided in detail in Fermani et al (68) and Huber et al (22).…”

Section: Methodsmentioning

confidence: 99%

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Primer Design for an Accurate View of Picocyanobacterial Community Structure by Using High-Throughput Sequencing

Huber

Cornejo‐Castillo

Ferrera

et al. 2019

Appl Environ Microbiol

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High-throughput sequencing (HTS) of the 16S rRNA gene has been used successfully to describe the structure and dynamics of microbial communities. Picocyanobacteria are important members of bacterioplankton communities, and, so far, they have predominantly been targeted using universal bacterial primers, providing a limited resolution of the picocyanobacterial community structure and dynamics. To increase such resolution, the study of a particular target group is best approached with the use of specific primers. Here, we aimed to design and evaluate specific primers for aquatic picocyanobacterial genera to be used with high-throughput sequencing. Since the various regions of the 16S rRNA gene have different degrees of conservation in different bacterial groups, we therefore first determined which hypervariable region of the 16S rRNA gene provides the highest taxonomic and phylogenetic resolution for the generaSynechococcus,Prochlorococcus, andCyanobium. Anin silicoanalysis showed that the V5, V6, and V7 hypervariable regions appear to be the most informative for this group. We then designed primers flanking these hypervariable regions and tested them in natural marine and freshwater communities. We successfully detected that most (97%) of the obtained reads could be assigned to picocyanobacterial genera. We defined operational taxonomic units as exact sequence variants (zero-radius operational taxonomic units [zOTUs]), which allowed us to detect higher genetic diversity and infer ecologically relevant information about picocyanobacterial community composition and dynamics in different aquatic systems. Our results open the door to future studies investigating picocyanobacterial diversity in aquatic systems.IMPORTANCEThe molecular diversity of the aquatic picocyanobacterial community cannot be accurately described using only the available universal 16S rRNA gene primers that target the whole bacterial and archaeal community. We show that the hypervariable regions V5, V6, and V7 of the 16S rRNA gene are better suited to study the diversity, community structure, and dynamics of picocyanobacterial communities at a fine scale using Illumina MiSeq sequencing. Due to its variability, it allows reconstructing phylogenies featuring topologies comparable to those generated when using the complete 16S rRNA gene sequence. Further, we successfully designed a new set of primers flanking the V5 to V7 region whose specificity for picocyanobacterial genera was testedin silicoand validated in several freshwater and marine aquatic communities. This work represents a step forward for understanding the diversity and ecology of aquatic picocyanobacteria and sets the path for future studies on picocyanobacterial diversity.

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Section: Discussionsupporting

confidence: 89%

Section: Methodsmentioning

confidence: 99%

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Primer Design for an Accurate View of Picocyanobacterial Community Structure by Using High-Throughput Sequencing

Huber

Cornejo‐Castillo

Ferrera

et al. 2019

Appl Environ Microbiol

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“…At first, we considered all data we gathered from the literature in our analyses. However, some of the studies performed in highly eutrophic environments have found extreme values of HB and HNF abundance, never reported before on the literature (i.e., Fermani et al, 2013 , 2015 ). As we did not found any equivalent conditions in the tropical dataset, and since we noticed that the data from those studies were outliers, we decided to disregard those values from all our analyses.…”

Section: Resultsmentioning

confidence: 70%

Coupling Between Heterotrophic Nanoflagellates and Bacteria in Fresh Waters: Does Latitude Make a Difference?

et al. 2016

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Recent studies reported comparatively lower heterotrophic bacteria (HB) abundances in tropical regions, indicating that factors involved in bacterial losses could be more relevant in the tropics. Heterotrophic nanoflagellates (HNF) are considered the main predators of HB in aquatic ecosystems, and one should expect higher abundances in the tropics because of differences in the food web configuration (absence of large daphnids). However, there are no comprehensive studies comparing HB and HNF abundances in a latitudinal gradient. We hypothesized that HB abundance would be lower in the tropics because HNF abundance would be higher, resulting in a tighter HNF–HB coupling. To test this hypothesis, we compiled a large dataset of HB and HNF abundances from tropical and temperate freshwater environments. We found that both HB and HNF abundances were lower in the tropical region, and that HNF-HB coupling does not differ between temperate and tropical regions. The lower HNF abundance and lack of coupling may be explained by a strong top-down control on HNF and/or their herbivory preference. Besides, no relationship was found between bacterial specific growth rate and either chlorophyll-a and HB abundance, indicating that bacterial losses may have an important role in tropical freshwaters. Thus, we found that HNF is likely not the main controllers of HB abundance, and that grazing by ciliates and cladocerans, together with the physiological effects of higher temperatures, may explain the high bacterial loss rates in the tropics.

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“…Croatia (Šolić et al 2010), and in many eutrophic lakes (Wieltschnig et al 2001, Zingel et al 2007, Fermani et al 2014. The weak coupling between HNF and bacteria results in most cases from the strong top-down control of ciliates on HNF.…”

Section: Eutrophication Effect On Carbon Transfer Among the Microbialmentioning

confidence: 99%

Eutrophication disrupts summer trophic links in an estuarine microbial food web

et al. 2019

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Eutrophication is the most widespread effect of urban development in coastal areas. To elucidate how nutrient loading affects the carbon pathways at the base of food chains, we quantified the carbon transfer among microbial components, from prokaryotes to microzooplankton. For this purpose, we performed two size-fractionation feeding experiments during late summer under moderate (N: 28.5 μM, P: 0.92 μM, Si: 45.8 μM) and severe (N: 173.9 μM, P: 3.5 μM, Si: 67.2 μM) cultural eutrophication in the Bahía Blanca Estuary (Argentina). In both experiments, prokaryotes were largely dominated by heterotrophic forms, small diatoms dominated among autotrophs, and heterotrophic nanoflagellates were the most abundant among protistan grazers. Under severe eutrophication, however, the average biomass was 75% lower for all autotrophic and heterotrophic components. Nutrient loading sustained a higher growth rate of heterotrophic bacteria and phytoplankton but implied poorer trophic transfer. Under moderate eutrophication, daily productivity of nanoplankton and bacteria grazed was 157% and 154%, respectively, while under severe eutrophication, this percentage dropped to 3.54% and 33.7%, respectively. In addition, under excess nutrient conditions, microzooplankton evidenced an active prey switching toward the most abundant prey (diatoms). Weak top-down control of bacterial biomass along with trophic decoupling between microzooplankton and nanoflagellates, constituted a dead-end of bacterial biomass under severe cultural eutrophication. This inefficient carbon transfer can potentially produce a positive feedback by exacerbating organic matter accumulation.

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Microbial abundance patterns along a transparency gradient suggest a weak coupling between heterotrophic bacteria and flagellates in eutrophic shallow Pampean lakes

Cited by 20 publications

References 82 publications

Primer Design for an Accurate View of Picocyanobacterial Community Structure by Using High-Throughput Sequencing

Primer Design for an Accurate View of Picocyanobacterial Community Structure by Using High-Throughput Sequencing

Coupling Between Heterotrophic Nanoflagellates and Bacteria in Fresh Waters: Does Latitude Make a Difference?

Eutrophication disrupts summer trophic links in an estuarine microbial food web

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